Population: 165,800,000
Capital: Islamabad

Political Rights Score: 6
Civil Liberties Score: 5
Status: Not Free


Pakistan in 2006 remained firmly under the control of a military government headed by General Pervez Musharraf. Despite facing opposition from both secular and Islamist political parties, pro-Musharraf forces continued to hold sway in national politics, and Musharraf worked to ensure his personal continuation in power through the planned 2007 presidential and parliamentary elections. In the absence of a completely independent legislature and judiciary, the media remained one of the only forums that provided oversight of official actions and policy. However, the government has become less tolerant of such criticism and, on a number of occasions, harassed or intimidated members of the press. A range of other human rights violations, including "enforced disappearances" and torture, as well as widespread legal and societal discrimination against women and religious minorities, continued to be reported. Modest legal reforms that ameliorated some of the worst forms of discrimination against women with regard to rape were enacted during the year. Sectarian and terrorist violence remained a concern, and fighting between government forces and local Taliban in the Pashtun tribal areas as well as separatists in Baluchistan province escalated in 2006, leading to hundreds of deaths and the displacement of thousands of civilians.

Pakistan came into existence as a Muslim homeland with the partition of British India in 1947. Following a nine-month civil war, East Pakistan achieved independence in 1971 as the new state of Bangladesh. The army has directly or indirectly ruled Pakistan for 31 of its 58 years of independence. As part of his efforts to consolidate power, the military dictator General Zia ul-Haq amended the constitution in 1985 to allow the president to dismiss elected governments. After Zia's death in 1988, successive presidents cited corruption and abuse of power in sacking elected governments headed by Benazir Bhutto of the Pakistan People's Party (PPP) in 1990 and 1996, and Nawaz Sharif of the Pakistan Muslim League (PML) in 1993.

After the PML decisively won the 1997 elections, Sharif, as prime minister, largely ignored Pakistan's pressing economic and social problems while attempting to undermine every institution capable of challenging him, including the judiciary and the press. However, when he attempted to reshuffle the army's leadership and fire the army chief, he was deposed in October 1999 in a bloodless coup. Chief of Army Staff General Pervez Musharraf then appointed himself "chief executive," declared a state of emergency, and suspended Parliament, the provincial assemblies, and the constitution. In December 2000, 18 of Pakistan's political parties, including archrivals PML and PPP, joined to form the Alliance for the Restoration of Democracy (ARD), an umbrella group calling for an end to military rule. However, Musharraf has been able to successfully neutralize Sharif and Bhutto, his primary political opponents, through a combination of court convictions and exile.

Musharraf's primary aim since gaining power has been to ensure a dominant role for the military after Pakistan made the nominal transition back to democratic rule. The controversial 2002 Legal Framework Order (LFO), which was intended as a vehicle for amending the constitution without the participation of Parliament, gave him effective control over Parliament and changed the electoral rules to the detriment of opposition parties. The regime also openly promoted progovernment political parties, such as the newly formed Pakistan Muslim League Quaid-i-Azam (PML-Q). In the 2002 parliamentary elections, no single party won a majority of seats; the PML-Q won 126 seats, while the PPP won 81 and the PML, 19. A coalition of six religious parties, the Muttahida Majlis-i-Amal (MMA), performed unexpectedly well, winning 63 seats in the national Parliament and a majority of seats in two provinces. With support from independents and deserters from the other main parties, the PML-Q was able to form a government; it then consolidated its position by winning a majority of seats in the 2003 Senate elections.

Parliament was deadlocked throughout most of 2003, with the main opposition parties insisting that Musharraf rescind the LFO, introduce legal and constitutional changes through the normal parliamentary process, and relinquish his position as army chief if he wished to continue as president. A deal brokered with the MMA enabled the government to pass a constitutional amendment in January 2004 legitimizing the coup; the government was then able to pass legislation in April 2004 establishing a powerful National Security Council (NSC), headed by the president, which further solidified the military's role in government. In a reversal of his pledge to the MMA that he would step down as army chief by year's end, Musharraf then announced in September 2004 that the need for stability required him to stay on in both roles. This decision was formalized when the Parliament passed the President to Hold Two Offices Act, enabling him to stay on as army chief until 2007. In reaction, the MMA launched nationwide protests and have continued to oppose the government.

In May 2005, Musharraf announced that he might stay on in both roles past 2007, when parliamentary elections were scheduled. Local council elections held in August and September were seen as a test of the government's commitment to allowing freer and fairer elections to take place. The elections were held on a nonparty basis with more than 218,000 candidates participating; in final results, PML-Q-backed candidates performed well in Punjab and Sindh, while nationalist parties scored gains in the North West Frontier Province (NWFP) and Baluchistan at the expense of MMA-backed candidates. However, opposition parties as well as monitoring groups expressed dissatisfaction with the conduct of the process. In addition to higher-than-usual levels of violence – there were over 60 election-related deaths and some 550 injured countrywide – numerous cases of pre-poll rigging, ballot stuffing, intimidation, and other forms of coercion and fraud were condemned by the independent Human Rights Commission of Pakistan (HRCP), the International Crisis Group (ICG), and others. With the moderate opposition parties having been further marginalized and with local government structures more firmly under the grip of his political allies, Musharraf remained well placed to continue in power.

While managing to contain the secular opposition, Musharraf has been less willing to rein in the Islamic fundamentalist groups with whom the military has traditionally had a close relationship. Although several groups have been banned since September 2001, when Musharraf pledged to support the United States in its antiterrorism efforts, and hundreds of activists have been periodically arrested, more than 40 groups continue to function under new names, and their leaders have generally not been prosecuted. The increased parliamentary presence of religious parties with ties to radical madrassas (religious schools) and militant groups suggests that the influence of the Islamists will continue to be strong. However, official tolerance for the activities of these groups declined somewhat following several assassination attempts against Musharraf and Prime Minister Shaukat Aziz in late 2003 and 2004. After the July 2005 London terrorist bombings, which involved several British citizens of Pakistani origin who had studied in Pakistan, Musharraf ordered a renewed crackdown on militant groups and madrassas, which further worsened the relationship between the government and the MMA. Nevertheless, many militant groups remain active, and sectarian violence, which kills and injures several hundred people each year, continues to be a concern. Particularly serious attacks in 2006 included a bomb attack in March that killed a U.S. diplomat and four others, and a suicide attack on a Karachi shrine in April that killed more than 50, including several Sunni religious leaders. Musharraf remains at risk for an assassination or coup attempt amid reports of growing disenchantment with his leadership within the military; in October, there was an explosion near his home, and rocket launchers were found nearby.

Fighting and unrest between government forces and tribal groups in Baluchistan, which was triggered by the rape of a female doctor allegedly at the hands of the army, escalated in early 2005, and the situation has steadily deteriorated since then. A separatist group, the Baluchistan Liberation Army (BLA), has stepped up its attacks on infrastructure (particularly gas pipelines) and development projects and staff, while local tribal leaders continue to demand greater political autonomy and control over the province's considerable natural resources. After a rocket attack targeted Musharraf in December 2005, he refused to engage Baluchi groups politically and initiated counterinsurgency paramilitary operations, which has led to increased human rights violations and a looming humanitarian crisis. The government declared the BLA a terrorist group in April 2006, and the army killed the 79-year-old Baluchi separatist leader Nawab Akbar Khan Bugti and a number of his followers in a counterinsurgency operation in August. Bugti's death led to increased political instability and rioting, with heightened tensions still simmering at year's end.

With both parliamentary and presidential elections planned for 2007, all political factions spent 2006 jockeying for influence and attempting to work the system to their advantage. Musharraf has made clear his interest in remaining president for another term, and in the face of a disunited opposition (which currently consists of the ARD and the MMA), he and his parliamentary allies are expected to win both sets of elections. The ARD has discussed whether to participate in or boycott the elections, but its unity has been shaken by rumors that PPP leader Benazir Bhutto has been in secret talks with the military government that would enable her to return to Pakistan and contest the elections. While Musharraf's position remained strong, his popularity continued to wane and the PML-Q has a minority in parliament; therefore, in order to ensure his reelection, in June 2006 Musharraf brought forward the date of the presidential vote (the president is chosen by a parliamentary electoral college) so it would be held while the current assemblies were still sitting.

The general has also been forging political deals with one of the main religious parties, the pro-Taliban Jamiat-e-Ulema Islam (JUI), in order to split the MMA and bolster his support, particularly in Baluchistan and NWFP, ahead of the key 2007 vote. The JUI was instrumental in helping to negotiate a peace accord reached between the government and a tribal Taliban council in North Waziristan in early September, under which authorities released a number of local fighters in exchange for a cessation of attacks on the army. While Musharraf hailed the deal as a success that would lead to greater stability along the Pakistan-Afghanistan border, critics alleged that it would lead to the Taliban gaining effective control on the ground in the Federally Administered Tribal Areas (FATA), and that it would not stop Taliban incursions over the border into Afghanistan. The latter thesis proved correct, with reports of more insurgents crossing the border following the deal. Analysts remained concerned that the influence of the Taliban was continuing to spread in northern Pakistan, particularly in the FATA, NWFP, and Baluchistan.

Political Rights and Civil Liberties

Pakistan is not an electoral democracy. Despite the election of a civilian National Assembly in October 2002, the Pakistani military, headed by General Pervez Musharraf, continues to wield effective control over the structures of government. The 1973 constitution provides for a lower National Assembly, which currently has 272 directly elected seats and 70 seats reserved for women and non-Muslim minorities, all elected for five-year terms; and a Senate, the majority of whose 100 members are elected by the four provincial assemblies for six-year terms. Shortly after the 1999 coup, Musharraf suspended the provincial and national assemblies, declared himself president, and in 2002 held a referendum that was widely regarded as rigged in order to extend his term as president. In preparation for national elections – after the coup, the Supreme Court mandated that they be held by October 2002 – Musharraf further strengthened the powers of the presidency and formalized the military's role in governance. The LFO gave him the right to unilaterally dismiss the national and provincial parliaments, as well as providing for a National Security Council dominated by military figures that would supervise the work of a civilian cabinet. The president is also elected for a five-year term by an electoral college that consists of the Senate, as well as members of the national and provincial assemblies.

The LFO also restricts certain individuals from standing for elected office, as well as restricting political parties in their choice of leadership. Some of these measures were explicitly aimed at preventing former prime ministers Benazir Bhutto and Nawaz Sharif from contesting the 2002 elections. Although the government lifted the long-standing ban on political rallies shortly before the elections, significant restrictions remained in place, and the ability of opposition parties to mount effective campaigns was circumscribed. In its statement on the elections, the HRCP noted that governmental machinery had been used to intimidate opposition candidates. The report of the European Union Election Observation Mission concluded that there had been "serious flaws" in the electoral process.

Since the election, secular opposition parties and their leaders have continued to face intimidation and harassment from intelligence agencies and other government organs. Javed Hashmi, the leader of the ARD alliance, who was sentenced to 23 years on sedition charges in April 2004 after reading an anti-Musharraf letter at a news conference, remained in jail throughout 2006. Prior to and during the 2005 local elections, a number of opposition candidates were abducted or otherwise intimidated, according to the ICG.

On the positive side, women and minorities now have enhanced representation in the Parliament. After repeated complaints by religious minorities, the government abolished the system of separate electorates in January 2002, enabling them to vote alongside Muslims and thus participate more fully in the political system. In addition, 10 seats in the reconstituted National Assembly were reserved for minorities and 60 were reserved for women. However, women continue to have difficulty voting and running for office in some parts of the country due to opposition by social and religious conservatives.

Pakistan's government operates with limited transparency and accountability. Since the 1999 coup, military officers have assumed an increasing role in governance through "army monitoring teams" that oversee the functioning of many civilian administrative departments. The army now has a stake in continuing to influence both commercial and political decision-making processes, as well as maintaining its traditional dominance over foreign policy and security issues. Serving and retired officers receive top public sector jobs in ministries, state-run corporations, and universities, and are given a range of other privileges. The effective functioning of the Parliament has been hampered by ongoing opposition boycotts, and many pieces of legislation have been pushed through with limited debate. According to the Economist, most important policies are introduced by presidential decree, as ordinances, and are renewed every four months if not formally passed into law by the rubber-stamp Parliament.

Corruption is pervasive at almost all levels of politics and government; Transparency International's 2006 Corruption Perceptions Index ranked Pakistan 142 out of 163 countries surveyed. Although Musharraf has publicly stated that eliminating official corruption is a priority, the National Anti-Corruption Strategy approved in 2002 focuses on politicians, civil servants, and businesspeople, while virtually ignoring military and security personnel. Corruption charges are frequently used as a tool to punish opposition politicians or to induce them to defect and join the PML-Q.

The constitution and other laws authorize the government to curb freedom of speech on subjects including the constitution, the armed forces, the judiciary, and religion; blasphemy laws have also been used to suppress the media. On numerous occasions, police, security forces, and military intelligence officers have subjected journalists to physical attacks, intimidation, or arbitrary arrest and incommunicado detention. In addition, Islamic fundamentalists and thugs hired by feudal landlords or local politicians continue to harass journalists and attack newspaper offices. Reporters in Sindh province faced threats and attacks from local authorities and political or tribal figures during the year. In total, more than 100 such instances were reported throughout 2006. Conditions for reporters covering the ongoing unrest in the tribal areas bordering Afghanistan were particularly difficult, with a number of local and foreign correspondents detained, threatened, or otherwise prevented from covering events there, either by the Taliban and local tribal groups or by the army and intelligence services. Reporter Hayatullah Khan, who was abducted in the semiautonomous North Waziristan tribal region in December 2005, was found dead in June 2006, while unknown assailants seized Dilawar Khan, a reporter for the BBC Urdu service based in South Waziristan, in November 2006. In a chilling trend, the young siblings of both men were also killed, apparently to threaten the journalists and their families.

While a number of journalists practice self-censorship, Pakistan continues to have some of the most outspoken newspapers in South Asia, and the broadcast sector has become considerably more diverse with the opening of a number of new private television stations. However, military authorities are using increasingly aggressive tactics to silence critical voices in the media. A number of journalists have been pressured to resign from prominent publications, charged with sedition, or arrested and intimidated by intelligence officials while in custody; a number of media outlets have also been temporarily banned from publishing or broadcasting. Musharraf himself has also contributed to an atmosphere that is inimical to free speech by making public threats against specific members of the press. Authorities have also used advertising boycotts to put economic pressure on publications that do not heed unofficial directives on coverage. Internews reported that at least 11 newspapers or magazines were denied state-sponsored advertising in 2006 for being critical of government policies. Authorities blocked access to certain websites, particularly those involving Baluchi nationalist issues, with several dozen blocked at various times during the year. In February, the decision of the Pakistan Telecommunication Authority (PTA) to block access to the hosting site blogspot.com was met with protests from the expanding community of Pakistani bloggers and from freedom of expression groups.

Pakistan is an Islamic republic, and there are numerous legal restrictions on religious freedom. Blasphemy laws provide for steep sentences, including the death penalty, for defiling Islam, the prophet Muhammad, and the Koran; in addition, injuring the "religious feelings" of individual citizens is prohibited. Instances of low-ranking police officials being bribed to file false blasphemy charges against Ahmadis, Christians, Hindus, and occasionally other Muslims have increased in recent years. Ahmadis consider themselves to be Muslims, but the constitution classifies them as a non-Muslim minority, and the penal code severely restricts Ahmadi religious practice. Authorities occasionally confiscate or close Ahmadi publications and harass journalists or printers involved in their production. To date, appeals courts have overturned all blasphemy convictions, but suspects are generally forced to spend lengthy periods in prison, where they are subject to ill-treatment, and they continue to be targeted by religious extremists after they are released. In an attempt to limit abuse of these laws, an amendment was enacted in 2005 requiring that a senior police officer investigate such charges. This led to a significant reduction in new blasphemy cases registered in 2006, according to the U.S. State Department's 2006 Report on International Religious Freedom.

Religious minorities also face unofficial economic, social, and cultural discrimination, and are occasionally subjected to violence and harassment. Attacks on places of worship and religious gatherings occur frequently, leading to the deaths of dozens of worshippers every year. The government often fails to protect religious minorities from sectarian violence, and discriminatory legislation contributes to a general climate of religious intolerance. In 2005, right-wing religious groups successfully lobbied the government to retain religious designations on Pakistani passports.

The government generally does not restrict academic freedom. However, student groups, some of whom have ties to radical Islamist organizations, violently attack or otherwise intimidate students, teachers, and administrators at some universities. According to the ICG, college students are now also required to sign affidavits declaring that they will not participate in any political activity, and this ban is selectively enforced against supporters of opposition parties. During the year, the government continued to implement reforms of the public education sector designed to minimize the teaching of religious intolerance. It also attempted to impose greater state control over the country's thousands of madrassas, or Islamic religious schools, by requiring registration, the use of a more modernized curriculum, an end to extremist recruitment, and the expulsion of foreign students. Girls' schools, particularly in NWFP, faced threats from religious extremists in 2006, leading some parents to withdraw their children.

The military government banned all public political meetings, strikes, and rallies in March 2000. Authorities regularly disperse protests using force and preemptively arrest political activists to prevent demonstrations from occurring. Some Islamist leaders have been held under house arrest or in preventive detention under the Maintenance of Public Order ordinance, which allows for three months' detention without trial. Laws governing sedition, public order, and terrorism have also been used to raid party offices and detain political activists and leaders in Punjab and Sindh.

Authorities generally tolerate the work of nongovernmental organizations (NGOs) and allow them to publish critical material. In recent years, Islamic fundamentalists have issued death threats against prominent human rights defenders and female NGO activists who work in rural areas. Parvez Aslam Choudhry, a prominent human rights lawyer who has defended several blasphemy suspects, was attacked and beaten by religious extremists in January 2006. Citing security concerns, during the latter half of the year the government prevented aid groups from operating in strife-torn Baluchistan, leading to a worsened humanitarian situation in the province by year's end.

Trade unions are independent. The law restricts the right to strike, and workers in certain essential industries face restrictions on bargaining collectively and generally cannot hold strikes. Despite legislation outlawing bonded labor and canceling enslaving debts, illegal bonded labor continues to be widespread, particularly in Sindh province. According to news reports, there is a growing trend involving bonded laborers who sell organs, particularly kidneys, in order to escape their servitude. The enforcement of child labor laws remains inadequate; recent surveys have indicated that there are at least eight million child workers in Pakistan, and those found employing children often avoid punishment.

The judiciary consists of civil and criminal courts and a special Sharia (Islamic law) court for certain offenses. Lower courts remain plagued by endemic corruption; intimidation by local officials, powerful individuals, and Islamic extremists; and heavy backlogs that lead to lengthy pretrial detentions. The military regime undermined the Supreme Court's reputation for independence in January 2000, when it ordered all high-ranking judges to swear to uphold the Provisional Constitutional Order issued by Musharraf. When the chief justice and a number of other judges refused, they were replaced. Since then, the courts have rejected subsequent challenges to the legality of military rule. A November 2004 ICG report drew attention to the fact that the executive has extended its influence over the judiciary by using the appointments system to remove independent judges, fill key positions with political allies, and reward those who issue judgments favorable to the government. However, the Supreme Court in particular does occasionally show sparks of independence.

Other parts of the judicial system, such as the antiterrorism courts, operate with limited due process rights. A 1999 ordinance vested broad powers of arrest, investigation, and prosecution in a National Accountability Bureau and established special courts to try corruption cases. Musharraf has used both selectively to prosecute rival politicians and officials from previous civilian governments. The Sharia court enforces the 1979 Hudood Ordinances, which criminalize nonmarital rape, extramarital sex, and several alcohol, gambling, and property offenses. They also provide for Koranic punishments, including death by stoning for adultery, as well as jail terms and fines. In part because of strict evidentiary standards, authorities have never carried out the Koranic punishments. Pressure to amend or do away with the ordinances, which are highly discriminatory toward women, has grown in recent years, and the Musharraf government has been generally supportive of such proposals. In November 2006, after many delays, limited progress was made to reverse some of the most negative provisions of certain ordinances, although activists complained that the government had caved in to pressure from religious conservatives and that the reforms were not sufficient.

Tensions between national and constitutional laws and the efforts of provincial assemblies to pass restrictive legislation based on Islamic values continue to be an issue. In July 2005, the NWFP assembly, which had previously passed legislation declaring Sharia to be the supreme law of the province, passed the Taliban-style Hisba (accountability) Bill, under which a watchdog agency would monitor and enforce adherence to Islamic values and practices. Musharraf then referred the legislation to the Supreme Court, which in August 2005 declared that large sections of the bill were unconstitutional and prohibited its implementation. However, in November 2006, a modified version of the bill was passed by the provincial assembly; critics expressed concern that the wording of the bill was intentionally vague and open to diverse interpretations. The Supreme Court issued a stay order in December to prevent the NWFP governor from signing the bill into law, and it remained unresolved at year's end.

The Federally Administered Tribal Areas (FATA) are under a separate legal system, the Frontier Crimes Regulation, which authorizes tribal leaders to administer justice according to Sharia and tribal custom. Feudal landlords and tribal elders throughout Pakistan adjudicate some disputes and impose punishments, including the death penalty or the forced exchange of brides between tribes, in unsanctioned parallel courts called jirgas. In April 2004, responding to growing concern over the potential for abuse inherent in this practice, the Sindh High Court issued a ruling that banned all trials conducted under the jirga system in the province. However, such judgments continue to take place.

Anecdotal evidence suggests that police continue to routinely engage in crime, use excessive force in ordinary situations, arbitrarily arrest and detain citizens, extort money from prisoners and their families, accept money to register cases on false charges, rape female detainees and prisoners, commit extrajudicial killings, and torture detainees (often to extract confessions). Political opponents, former government officials, and other critics of the regime are particularly at risk of arbitrary arrest or abduction, torture, "disappearance," and denial of basic due process rights at the hands of military authorities, according to Human Rights Watch and local NGOs. Progress on creating a National Human Rights Commission that is empowered to monitor and investigate cases of abuse and to redress grievances remained slow during the year.

The HRCP has noted a marked increase in the number of people being illegally detained by state agencies, sometimes for extended periods of time, citing reports that more than 600 have disappeared since 2002. Initially most of those detained were suspected of links to radical Islamist groups, but more recently Baluchi and Sindhi nationalists, government critics, and some journalists, researchers, and social workers have also been targeted. Although intelligence services operate largely with impunity and outside the purview of the judicial system, in October 2006, the Supreme Court took up several cases of disappearance and ordered the government to speed up the process of producing the incarcerated men. As a result of the court decision, approximately 20 men were freed by year's end.

Prison conditions continue to be extremely poor, with overcrowding a particular problem, although authorities have taken some steps to ameliorate the situation. A January 2005 Amnesty International report noted that the Juvenile Justice System Ordinance of 2000 remains largely unimplemented and that numerous children continue to be jailed alongside adults, heavily fined, and sometimes sentenced to death.

Press reports indicate that there may be as many as 200,000 armed militants currently active in Pakistan. These extremists carry out terrorist attacks within Pakistan and in neighboring countries, including assassination attempts and suicide bombings directed at foreign, Shia, and Christian targets, which kill at least several hundred civilians each year. Sunni and Shia fundamentalist groups continue to engage in a cycle of retaliatory sectarian violence, mostly bomb attacks against mosques, other places of worship such as shrines, and religious processions or gatherings. The New Delhi-based South Asia Terrorism Portal (SATP) reported that 201 people were killed and 349 were injured as a result of sectarian violence in 2006, roughly the same number as the previous year. About 50 people were killed, including three prominent religious leaders, and 100 injured when a suicide bomber attacked a Sunni prayer service in Karachi in April.

Operations by the Pakistani army and security forces (with support from the United States) against foreign militants in the tribal areas have been ongoing since 2002, and cases of human rights abuses committed during the course of these operations, including arbitrary arrest and detention, the destruction of property, the death or displacement of civilians, and extrajudicial executions, continue to be reported. The focus during 2006 was on North Waziristan, where the army deployed additional troops in an effort to root out Islamist militants. Meanwhile, after striking a deal with the army in late 2004, local Taliban militants have strengthened their hold over the South Waziristan agency, imposing strict behavioral codes and killing progovernment political and religious leaders, including 150 tribal elders in the past three years. In late October, air strikes destroyed a madrassa in Bajaur agency, killing around 80 people; angered locals then staged mass demonstrations. Possibly in response, in early November a suicide bomber struck an army training school in NWFP, killing 42 soldiers. Overall, the SATP reported that 1,471 people were killed in terrorist or insurgent-related violence in 2006, including 608 civilians, 325 security force personnel, and 538 militants.

Beginning in early 2005, Baluchistan nationalist groups demanding increased autonomy and control over profits gained from natural resources have increased their attacks on gas pipelines and other infrastructure, and the army has stepped up military reprisals in response, leading to violence, instability, human rights violations, and the displacement of thousands of civilians. The killing of the elderly rebel tribal leader Nawab Akbar Khan Bugti by the army in August 2006 triggered violent riots and strikes, inflaming Baluchi nationalist feelings still further.

In an atmosphere in which the rule of law is weakly enforced and the military has expanded its control over economic resources, land rights are at risk. According to a Human Rights Watch report, tenant farmers in the Okara district of Punjab who have refused to cede their land rights to the army have faced besiegement, arbitrary arrest and detention, torture, "forced divorce," dismissal from employment, and, in the most extreme cases, murder. The growing dominance of the military over economic and commercial activity more generally has been cause for concern.

A combination of traditional norms, discriminatory laws, and weak law enforcement continues to contribute to a high incidence of rape, domestic violence, acid attacks, and other forms of abuse against women; according to the HRCP, up to 80 percent of women are victims of such abuse during their lifetimes. Female victims of rape or other sexual crimes are often pressured by police not to press charges, and are sometimes pressured by their families to commit suicide. Gang rapes sanctioned by village councils as a form of punishment for crimes committed by the targeted woman's relatives continue to be reported, despite the fact that harsh sentences have been handed down against the perpetrators in some cases. In 2005, an outcry erupted over Musharraf's comments that for some high-profile victims – Shazia Khalid, a doctor in Baluchistan who was raped in January and subsequently fled the country after being pressured by the government; and Mukhtaran Mai, who was gang-raped on the orders of a village council in 2002 and initially denied an exit visa to travel to the United States in June 2005 – rape had become a "money-making concern."

Under the discriminatory Hudood Ordinances, women can be charged with adultery or other sexual misconduct arising from rape cases or alleged extramarital affairs; thousands of women (an estimated 80 percent of the female prison population) have been incarcerated as a result of being wrongfully charged. The threat of being charged with adultery may prevent some women from reporting rape. In an attempt to reduce abuse of the ordinances, the government passed legislation in 2005 requiring a court order before a woman can be detained under such charges, which led to a significant decline in the number of new cases filed in 2006. In July 2006, Musharraf ordered the release on bail of all women held under the ordinances, and according to local NGOs, approximately 1,200 women had been released by the time the measure lapsed in November. More extensive reform of the ordinances has proved considerably harder to implement due to opposition from religious parties, who hold some power in parliament. However, after watering down initial drafts, the government was able to pass the Women's Protection Bill in November, which reformed some of the worst aspects of Hudood. A woman is no longer required to produce four Muslim male witnesses in order to prove rape, and judges can now try rape cases under criminal rather than only under Islamic law. However, extramarital sex is still criminalized, and marital rape is not recognized as a crime.

According to the HRCP, at least 565 women were killed by family members in so-called honor killings in 2006, and many more are otherwise humiliated or mutilated. Usually committed by a male relative of the victim, honor killings punish women who supposedly bring dishonor to the family. Government-backed legislation introducing stiffer sentences and the possibility of the death penalty for those convicted of honor killings was signed into law in January 2005. However, given a prevailing environment in which authorities generally do not aggressively prosecute or convict the perpetrators of violence against women, activists questioned the effectiveness of the bill. The tribal practice of vani, in which women are offered in marriage to the male relatives of victims killed by their own family members in order to settle a potential feud, continues to take place in certain parts of rural Pakistan, although there is growing opposition to the practice by the women themselves as well as social activists and religious scholars. It was declared illegal by the Supreme Court in 2004, and in a landmark December 2005 judgment the court ordered local police to offer women protection.

Pakistani women face unofficial discrimination in educational and employment opportunities, and the trafficking of women and children remains a serious concern, with females being trafficked or sold for the purposes of forced labor, sexual exploitation, or marriage to significantly older men. Children's access to education and health care continues to be inadequate, with low numbers for both school attendance and literacy, despite the presence of a number of local and international NGOs that work to address such problems.

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