Indonesia, the world's largest Muslim-majority nation, is also an intensely diverse country whose citizens are drawn from an estimated 300 separate ethnic groups, speaking different languages and practising multiple religious faiths. While the country is often held up as a model of religious tolerance and democracy, alarming instances of intolerance, which sometimes spilled into violence, shows that the reality is far removed from the political platitudes.

There were numerous examples throughout the year. Members of Indonesia's Ahmadiyya community, a Muslim community branded heretics by religious conservatives, continued to face persecution. In April, members of fundamentalist group Islamic Defenders Front (FPI) attacked an Ahmadi mosque in Singaparna, West Java, according to the Asian Human Rights Commission (AHRC), which contends that police did little to stop the damage.

That same month, the AHRC says FPI members forced an Ahmadiyya religious leader on Batam Island to sign an agreement to stop holding religious activities. In July, local media reported that 'an angry mob' attacked and injured three Ahmadis in Bogor. Other Ahmadiyya communities continue to be marginalized. Local media reported that 120 members of the Ahmadiyya community remain displaced in West Nusa Tenggara province, seven years after a mob attacked and burned their homes. They are unable to obtain basic identity cards, preventing them from accessing needed health and education services.

A report by Ahmadiyya advocacy group Lajnah Imaillah, submitted to the UN's Committee on the Elimination of Discrimination against Women (CEDAW) in July, outlined health concerns for a group of displaced Ahmadis who had fled violence from their homes in West Nusa Tenggara province. Some children from a group of 170 people living in temporary shelters on Lombok island were suffering from malnutrition, while others had dropped out of school.

Rights groups also called on authorities to stop attacks against minority Shi'a Muslims. In July, a Shi'a cleric from Madura Island was convicted of blasphemy for his religious teachings. An August incident left one Shi'a man dead in the same community after an attack in which a mob also burned down 35 homes belonging to Shi'a families. By the start of 2013, rights groups said local authorities were threatening the families already displaced by the violence with forced eviction.

Persecution against Christians also continued in parts of Indonesia, with groups blocking some congregations from holding religious services. In April, for example, local officials in an area outside Jakarta obstructed 100 members of the Filadelfia Batak Christian Protestant Church from worshipping. In 2009, local authorities stopped the planned construction of a church there, and the congregation has faced continuous opposition.

Overall, the Jakarta-based Setara Institute for Democracy and Peace recorded 264 cases of violations against religious freedoms during 2012 – a figure that has risen steadily over the last six years.

Rights groups say such persecution against religious minorities continues to occur in part because of a weak government response. For example, authorities have encouraged Christian and Shi'a communities to relocate, while court prosecutions against perpetrators of violent attacks are rare.

In July's CEDAW session examining Indonesia, the country's National Commission on Violence Against Women (Komnas Perempuan) warned that acts of intolerance against religious minorities could see an increase in violence against women in particular. Women from religious minorities face additional threats of rape and sexual intimidation even after the attacks, while those driven into shelters, as with the Ahmadiyya communities in West Nusa Tenggara, have lost their jobs and been prevented from registering their marriages.

In its concluding statement, the committee expressed deep concern about the pressures faced by rural and indigenous women. Women from rural settings were much less likely to be able to give birth in a health facility than their urban counterparts, a worrying problem that directly affects uneven maternal mortality rates, the committee stated.

Overall, Indonesia has made progress in lowering its maternal mortality rate, from a baseline of 390 deaths per 100,000 live births to 228, according to the government's Millennium Development Goals (MDGs) update last year. The goal is to reach 102 deaths per 100,000 live births in 2015. However, the results are uneven across the vast archipelago, with troubling differences between urban areas and the rural villages where many minority and indigenous women live. The discrepancy can be blamed in part on a weaker health system in outlying areas.

Indonesia's often heavy-handed crackdown on the movement for autonomy and self-governance in West Papua continued to have detrimental impacts on indigenous Papuans in the country's easternmost provinces.

In June, police shot and killed independence activist Mako Tabuni, whose death triggered angry demonstrations. Police claim the vice-chairman of the National Committee for West Papua (KNPB) violently resisted arrest, but activists and rights groups dispute this. Also that month, KNPB leader Buchtar Tabuni was arrested after police accused his organization of engaging in violence.

Throughout 2012, activists and rights groups accused police and military of employing intimidation tactics against activists, including arbitrary arrests, shootings and torture. In a June report, the Commission for Missing Persons and Victims of Violence (Kontras) outlined what it said was a drastic increase in reported torture incidents over the past 12 months, predominantly at the hands of police. The rights group said they had recorded 86 allegations of torture – triple the previous total. Roughly 40 per cent of reported victims were from the Papuan provinces.

The continuing conflict in West Papua is exacerbating what is already a worrying health situation for civilians. According to Indonesia's National AIDS Commission, AIDS prevalence rates are at least 15 times higher than the national average. This suggests a need to step up awareness and education efforts in high-risk areas. At a national level, heightened HIV infection rates are generally found in traditionally high-risk groups. However, in Papua, health professionals say the problem is more widespread across the general population. At the same time, NGOs, including those working in the health sector, say the authorities have made it increasingly difficult to work in the area, which suggests that West Papua's political stability will be an important determinant in changing health outcomes for minority groups.

Cases of land conflict between private companies and indigenous communities continued through the year. Protesters have often found themselves on the receiving end of excessive police force when staging demonstrations. In February 2012 for example, police shot and injured five farmers in Sumatra's Riau province. The AHRC said the farmers were peacefully protesting against a palm plantation firm.

The national government's broad development plans seem likely to be a source of future conflict if not handled carefully. Indonesia's Economic Master Plan (MP3EI) seeks to stimulate growth through a focus on so-called 'economic corridors' – clustering and connecting industrial and special economic zones throughout the country. It is crucial that indigenous groups themselves are included in any such planning that affects their land and livelihoods; failure to do so could instead increase tensions with affected groups.

In May, Indonesia was subject to scrutiny as part of the UN Human Rights Council's UPR process. Member states urged Indonesia to ensure that perpetrators of assaults against religious minorities were brought to justice and to ensure the rights of indigenous peoples. But some rights groups were disappointed by Indonesia's response to the UPR, which included a passage stating that 'given its demographic composition, Indonesia ... does not recognize the application of the indigenous people concept as defined in the UN Declaration on the Rights of Indigenous Peoples in the country'.

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