Indonesia hosted more than 120,000 refugees and asylum seekers at the end of 2000. The vast majority, an estimated 120,000, were East Timorese. Of those, all but 10,000 were believed to be in the Indonesian territory of West Timor. They had been there since soon after East Timor gained independence from Indonesia in late 1999.

In addition to the East Timorese, 415 refugees recognized by the UN High Commissioner for Refugees (UNHCR) and 373 asylum seekers were in Indonesia at year's end. All except 52 arrived during 2000. Most were from Iraq and Afghanistan, while others were from Iran, Somalia, Liberia, Sierra Leone, and Algeria.

Indonesia is not a signatory to the UN Refugee Convention and has no system for granting refugee status. However, Indonesian authorities permit asylum seekers to remain in Indonesia while UNHCR assesses their claims. Persons recognized by UNHCR as refugees are permitted to remain pending identification of a durable solution.

At the end of 2000, an estimated 750,000 to 850,000 Indonesians were internally displaced in 18 of Indonesia's 26 provinces. These included 215,000 to 285,000 persons in Maluku, 207,000 in North Maluku, 110,000 to 130,000 in Southeast Sulawesi, 73,000 in Central Sulawesi, 60,000 to 70,000 in West Kalimantan, 36,000 in North Sulawesi, 30,000 in North Sumatra, 20,000 in Java, 17,000 in Irian Jaya (West Papua), 15,000 in South Sulawesi, and at least 8,000 in Aceh. Thousands more were displaced elsewhere in Sumatra and on the islands of Nusa Tenggara.

About 6,000 Indonesian refugees from the province of Irian Jaya were living in Papua New Guinea at year's end. About 150 Indonesian Acehnese were refugees in Malaysia, while at least another 500 Acehnese lived there in refugee-like circumstances.

The U.S. Committee for Refugees (USCR) conducted two site visits to Indonesia during 2000 to assess the situation of refugees and internally displaced persons there. USCR's findings and recommendations were presented in an issue paper entitled, Shadow Plays: The Crisis of Refugees and Internally Displaced Persons in Indonesia, published in January 2001.

Pre-2000 Events

Indonesia's longtime president, Suharto (who, like many Indonesians, uses only one name), resigned in 1998. He was replaced by his hand-picked successor, B.J. Habibie. Economic and political discontent, ethnic violence, and separatism throughout the archipelago were the principal causes of Suharto's fall from more than 30 years in power. The political change, however, did not diffuse tensions, and 1999 saw continued violence.

The most high profile of Indonesia's regional conflicts was the bloodshed (and related displacement) leading up to and following East Timor's September 1999 refer endum on independence from Indonesia. Anti-independence militia, backed by the Indonesian army, used violence and intimidation in an attempt to coerce East Timorese into voting for autonomy within Indonesia rather than independence. Defying the intimidation, East Timorese voted overwhelmingly for independence. Afterwards, the militia began a rampage throughout the territory, destroying entire villages and causing widespread death and displacement. An Australian-led international peacekeeping force was eventually sent to quell the violence. (The international force was replaced by a UN transitional authority – which includes peacekeepers – in March 2000.)

In October 1999, the upper house of parliament elected Abdurrahman Wahid, a Muslim cleric known as "Gus Dur," as Indonesia's fourth president. Megawati Soekarnoputri (daughter of Indonesia's first president, Sukarno) was subsequently elected vice president.

Wahid announced that his top priorities would be to ease sectarian violence and to maintain the "territorial integrity" of Indonesia. Although Indonesia has the largest Muslim population of any country, it is not an Islamic state. With 360 tribal and ethno-linguistic groups and more than 250 different languages and dialects, Indonesia has experienced separatist movements in several provinces.

With the status of East Timor resolved before he took office, Wahid encountered the strongest separatism from Aceh, in the far west, and from the country's easternmost province, Irian Jaya. Other regions experienced religious and ethnic violence.

In late 1999, Indonesia adopted a law on regional autonomy for its provinces, to take effect on January 1, 2001. The law attempts to address complaints of inequitable resource sharing between Jakarta and the provinces.

Events of 2000

The year saw continued violence throughout Indonesia, leading to unprecedented levels of internal displacement and the continued inability of East Timorese refugees to return home. By year's end, Wahid was struggling for his political survival amid threats of impeachment.

Indonesia's civil and military leaders sought to prevent several provinces from following East Timor's lead. While most, if not all, of the separatist movements in Indonesia predated the 1999 referendum in East Timor, the referendum gave new hope to those with similar aims in other regions. Such regions share many characteristics with East Timor. In some cases, they share a history in which Indonesia's right to sovereignty over their region is at least questionable. In many cases, they share an enemy, real or perceived – the Indonesian military. They also share hostility toward "transmigration" – a long-standing governmental program by which Indonesians from crowded islands, primarily Java, are given land and economic incentives to relocate to less populated areas.

Regions with little or no separatist sentiment also experienced turmoil during the year, usually as a result of religious or ethnic hostility. Many Indonesians and others believe most of the turmoil was political at root, as military and civilian opponents of the Wahid government attempted to destabilize his regime.

In many areas of displacement, the government provides temporary accommodation, rice, and small amounts of cash to displaced persons. Yet, many factors have prevented Indonesia from effectively addressing the displacement crisis. As a result, most assistance to the displaced comes from international and local nongovernmental organizations (NGOs), as well as UN agencies.

In many areas, the displaced live in conditions that, while not adequate for the long term, are not desperate. In other areas, particularly in the Moluccas, conditions are more critical, with reports of serious malnutrition and disease.

In some cases, the Indonesian government has relocated displaced persons to temporary or long-term sites. Some NGOs, including USCR, have expressed concern that conditions at some of the new sites have not been suitable.

Late in the year, Indonesia's transmigration minister announced that the government had terminated the regular inter-island transmigration program. He said the government would instead focus on local transmigration programs, including the relocation of internally displaced persons. Many Indonesians and international aid workers believe transmigration has been one of the main factors behind the ethnic and religious violence.

East Timorese Refugees in West Timor

At the end of 2000, reliable estimates of the number of East Timorese refugees remaining in West Timor were difficult to obtain. UNHCR's official estimate was 110,000 (despite its estimate that 120,000 remained at the end of 1999 and that more than 40,000 repatriated during 2000). The Indonesian government's estimate was closer to 125,000, while estimates from other sources were as low as 60,000.

Pro-Indonesia militia still held sway in the territory, and virtually no international aid agencies, including UNHCR, were assisting the refugees as a result of the September 2000 deaths of three UNHCR workers. Despite continued pressure by the international community, Indonesia has been unable to disarm the militia and ensure the refugees' return.

Following the September 1999 referendum in East Timor, as many as 290,000 persons fled – or were forcibly moved by pro-Indonesia militia – to camps and settlements in West Timor. UNHCR estimated that approximately 40,000 of those 290,000 had transmigrated from other parts of Indonesia (many of whom soon returned to Java or other islands), leaving 250,000 East Timorese refugees in West Timor. Some 130,000 repatriated before the end of 1999.

The refugees were comprised of several groups. Approximately 14,000 were Indonesian civil servants and their families (about 70,000 persons). Another 24,000 were members and families of the Indonesian armed forces, known as TNI. Of the 14,000 civil servants, about 6,000 chose to relocate to other parts of Indonesia, leaving about 8,000 in West Timor. While some of them may have wished to return to East Timor, their decision was complicated by the fact that they could only remain Indonesian civil servants and continue drawing their salaries (or pensions) if they remained in Indonesia. The Indonesian government has explored ways to integrate some of them into the local civil service in West Timor.

Many of the TNI members and families may be kept on active duty, either in West Timor or other areas of Indonesia. The Indonesian government has explored demobilization and vocational training for those within a few years of retiring, who would likely stay in West Timor. Still others are expected to resign and repatriate to East Timor if their safety can be assured.

The remaining East Timorese in West Timor include at least three groups whose numbers are unknown: anti-independence militia members (or former militia members) and their families; East Timorese who supported autonomy over independence; and pro-independence East Timorese – the group believed to be "held hostage" by the militia. Efforts to register the refugees and identify their preferences have failed – in part because of the continued climate of violence.

Militia leaders, who openly roam the camps, are hostile toward UNHCR's efforts to educate the refugees about conditions in East Timor and to help them return. UNHCR has been forced to conduct what it calls "snatch and run" operations to get refugees out of the camps before the militia members can act.

In February 2000, Indonesian police held at gunpoint workers from UNHCR and the International Organization for Migration (IOM) while they were escorting refugees back to East Timor.

In June and July, UNHCR twice suspended (and later resumed) operations in certain camps because of increased violence. In late July, armed militiamen who had crossed the border from West Timor into East Timor killed a UN peacekeeper from New Zealand. He was the first UN peacekeeper to be killed in the territory. Indonesia once again announced plans to disarm the militia and close the camps by repatriating or locally settling all refugees.

UNHCR suspended operations in West Timor in late August after a violent attack against three staff who were distributing plastic sheeting to refugees. It resumed activities six days later after Indonesian authorities arrested two of the alleged assailants and agreed to increase security for humanitarian workers.

The resumption was short lived. On September 6, thousands of militia-led rioters stormed the UNHCR office in Atambua (near the East Timor border) and killed three UNHCR staff. Within the next two days, after obtaining permission from the Indonesian government, UN peace keepers in East Timor entered West Timor and evacuated all foreign and most local aid workers. The Indonesian government subsequently arrested six suspects in the murder. It charged three with manslaughter and three with aggravated manslaughter, setting a trial for January 2001.

At the time of the killings, more than 120 incidents of harassment and violence against aid workers and refugees had been recorded since UNHCR established a presence in West Timor a year earlier.

In September, Indonesia and the UN signed an agreement to work together to resolve the fate of the remaining refugees. Among other things, Indonesia proposed moving refugees to Wetar, an island north of East Timor.

Indonesia also established an "Inter-Ministerial Task Force" (SATGAS) to plan a solution for the refugees. Between September and the end of the year, SATGAS coordinated the voluntary repatriation of some 4,000 persons (800 families). The returnees were met at the East Timor border by staff of the UN Transitional Authority in East Timor (UNTAET), the UNTAET Peacekeeping Force, UNHCR, and IOM. Those organizations ensured the civilian status of the refugees, verified the voluntariness of their return, and provided transportation to their villages of origin.

According to UNHCR, a total of 40,270 East Timorese repatriated from West Timor during the year.

In October, Indonesia took several other steps toward pacifying the international community, including arresting militia leader Eurico Guterres (for the second time) and approving a visit to West Timor by a delegation of the UN Security Council.

In early November, one international NGO, Church World Service, reopened its programs in West Timor, noting that no aid had reached the camps for nearly a month and that conditions were likely desperate. The agency said the reopening was largely possible because its staff were all Indonesian and Timorese. On November 21, the UN Security Council mission that visited West Timor recommended that UN security experts be sent to determine whether it was safe for UN staff to return. No such assessment had occurred by year's end.

The refugees remain concentrated in three main areas: Kupang (the capital of West Timor, near the western tip of the island), Kefamananu (in the central part, outside of the East Timorese enclave of Oecussi), and Belu District, particularly Atambua (near the border with East Timor).

The camps vary by size and location. Although the three major Kupang-area camps are large, others are village-like settlements of only a few families. In Bela District, refugees are in more than 200 sites. While some camps are comprised of converted buildings, others consist of straw huts or tents with plastic sheeting. An unknown number of refugees live in the homes of family members or friends.

UNHCR estimated that at least 10,000 East Timorese were elsewhere in Indonesia at the end of 2000. Some of those, having voluntarily re-availed themselves of Indonesia's protection, were considered to be internally displaced persons. Others were still considered to be refugees. Following the refugees' initial forced movement into West Timor, the Indonesian government may have forcibly transmigrated some of them to other islands. Others voluntarily relocated from West Timor. While they may have supported East Timor's independence, they may fear returning to East Timor because of the ongoing threat of militia violence.

Religious Violence in the Moluccas

Of the estimated 800,000 internally displaced persons in Indonesia at the end of 2000, the greatest numbers – more than 400,000 – were in the provinces of Maluku and North Maluku (each of which contains several islands, collectively comprising the island chain known as the Moluccas). Violence between Christians and Muslims, which began in both provinces in 1999, continued throughout 2000. By the end of the year, some 5,000 Moluccans were believed to have died since the violence began. The fighting was particularly fierce in and around the city of Ambon in Maluku Province.

In addition to national politics, local factors have played a large role in the strife between two religious communities that have coexisted peacefully in Indonesia for decades. Members of both communities have been both the perpetrators and the victims of the violence.

Although the violence in the Moluccas subsided near the end of 2000, the situation remained tense, particularly in Ambon. Sniper activity and other outbursts continued taking lives and causing people to flee. In many areas, physical barriers remained between Christian and Muslim communities. Members of the Laskar Jihad, a Java-based Muslim warrior group, reportedly still had posts and checkpoints in all inner-city Muslim neighborhoods.

In North Maluku Province, nearly all of the displaced persons were from within the province, primarily the island of Halmahera. Some were transmigrants from other areas, including Java. Many persons from North Maluku had also fled to other areas of Indonesia. The North Maluku island of Ternate had been virtually emptied of its Christian population by the end of 2000, with many Christians fleeing to Manado, a Christian city in North Sulawesi. In late June, about 500 Moluccan refugees were missing and presumed dead when an overcrowded ferry disappeared at sea en route to Manado.

A small number of international NGOs, UN agencies, and local NGOs assisted the displaced in the Moluccas. Throughout the year, these agencies struggled to maintain operations in the midst of difficult security conditions, with most of those in Ambon at least temporarily suspending operations.

Many camps in the Moluccas are comprised solely of Muslims or Christians, although others are mixed. The locations range from concrete buildings to mountainous jungles. In the latter, malnutrition and disease have been serious problems.

Uprooted Acehnese

At the end of the year, at least 8,000 persons were displaced within Aceh, on the northern tip of the Indonesian island of Sumatra. As in 1999, the level of displacement in Aceh fluctuated widely, from approximately 4,000 in January to some 80,000 in August. At year's end, the violence in Aceh intensified, despite a formal "humanitarian pause" in the fighting.

The Acehnese have sought independence for more than 120 years, first from Dutch colonizers and later from Indonesia. An armed separatist movement known as GAM (the Free Aceh Movement) has been active in the province for more than 25 years. The Acehnese claim widespread human rights abuses by the Indonesian military and police – including killings, torture, rape, and the burning of homes and shops.

During 2000, as the deaths and disappearances of human rights activists increased (and as the bodies of the dead showed signs of torture), international NGOs increased their calls for an end to the violence and for bringing those accused of abuses to justice.

President Wahid announced in May that his government and GAM's leadership (based in Sweden) had reached an agreement on a "humanitarian pause" to the violence in Aceh. The pause, strongly opposed by the Indonesian military, commenced on June 2 for an initial period of three months. The agreement earmarked funds for humanitarian assistance to the displaced and provided for a monitoring team to review the provision of such assistance.

The displaced live in and around mosques, schools, and other buildings in Aceh, in conditions ranging from fair to poor. Acehnese student groups, active in the campaign for a referendum, provide logistical support for the camps and organize small amounts of assistance. Most assistance comes from private businesses and local NGOs, with a minimal amount coming from the government, primarily through the Indonesian Red Cross.

In October, local NGOs reported that some 16,000 of the displaced persons in Aceh (roughly half at the time) were Javanese transmigrants, with the rest being ethnic Acehnese.

Displaced Acehnese in the Pidie area were reportedly short of food and suffering numerous health problems. Student groups had requested assistance from the local community, but widespread poverty hindered such efforts.

As a result of increased violence, including attacks on their local staff, international NGOs had to scale back or suspend their work in Aceh during the year.

In August, three local staff of Oxfam were seriously injured in an attack that also took the lives of two displaced persons. A police and military patrol had chased suspected GAM rebels into a displaced persons camp in West Aceh, where the conflict escalated. Police officers reportedly beat the Oxfam workers after they failed to show identification documents.

The humanitarian pause was extended through January 2001, with the possibility of further extensions. However, the first seven months of implementation had failed to reduce the violence, death, and displacement. At the end of the year, a referendum on Aceh's independence seemed unlikely. Although the government planned to provide greater autonomy for the region, most Acehnese said such status would be meaningless.

In addition to the displaced within Aceh, thousands of persons have fled Aceh for the nearby province of North Sumatra, particularly the city of Medan. At the end of the year, an estimated 30,000 persons were displaced in North Sumatra. The displaced included not only native Acehnese but also Javanese transmigrants, many of whom said they fled threats and abuse from native Acehnese.

Irian Jaya (West Papua)

The province of Irian Jaya hosted some 17,000 displaced persons at the end of 2000. At least half were from Irian Jaya itself; others were from the Moluccas and elsewhere. Irian Jaya also absorbed the return of some Irianese (Papuan) refugees from neighboring Papua New Guinea. A resistance movement has operated in Irian Jaya since Indonesia took control of the region in 1963.

In 1999, Wahid said he would begin calling the province West Papua, to reflect the wishes of many of its people. However, the Indonesian parliament has not formally adopted the name, and Wahid has said that the name has not been officially changed.

At a June 2000 congress in Jayapura, the Irian Jaya capital, more than 500 tribal leaders declared the independence of West Papua and called for international recognition of their sovereignty. Wahid attempted negotiations, but the talks broke down and violence soon erupted again.

In early October, violence between police and pro-independence Papuans in the town of Wamena caused the deaths of 26 people and led more than 10,000 civilians to seek shelter. Many were in military and police posts, while others were in mosques or churches. Wamena was virtually emptied of its inhabitants. Most or all of the displaced were believed to be transmigrants. Weeks after the incident, international NGOs still did not have access to the displaced. A government official said the displaced were in squalid conditions and faced hunger if rice did not reach them soon.

At the end of the year, Irian Jaya also hosted nearly 4,000 displaced persons from the Moluccas. Most were on a relatively inaccessible island off Sorong, on the western tip of Irian Jaya. A large number of Moluccan families have been in Sorong for generations, making it a logical destination for persons fleeing the sectarian strife. However, much of the Sorong community was reportedly unhappy with the influx. Some of the displaced moved on to Tual in Southeast Maluku.

At the end of 2000, some 6,000 Irian Jayan refugees remained in Papua New Guinea.

Violence and Displacement Elsewhere

The island of Sulawesi hosted more than 250,000 displaced persons at the end of 2000. The largest number, as many as 130,000, were in Southeast Sulawesi Province, including the island of Buton. According to NGOs, conditions there ranged from fair to poor. Some displaced persons had reportedly purchased land, while the government had relocated others to areas not suitable for long-term settlement.

In Central Sulawesi Province, some 73,000 persons were displaced as a result of Muslim-Christian clashes in and around the town of Poso. The clashes, though linked to local causes, were related to the religious violence in the Moluccas.

The violence in Poso began in December 1998, with other significant occurrences in April and May 2000. The May events left 98 people dead and about 4,000 homes burned or destroyed. According to a report by InterNews Indonesia and the Association for Independent Journalists, the nature of the attacks led to speculation that members of the armed forces were involved.

Most of the displaced in camps in Poso and Palu were Muslim. In Tentena, about an hour from Poso, most of the displaced were Christian. University students organized much of the assistance, which was also provided by churches, local governments, and a few international agencies.

At the end of the year, an estimated 63,000 persons were internally displaced in the province of West Kalimantan on the Indonesian part of the island of Borneo. The vast majority of the displaced were ethnic Madurese from the coastal district of Sambas, which has experienced sporadic ethnic clashes since late 1996.

The Madurese are from the Indonesian island of Madura, off the coast of East Java. In the 1960s, Suharto began moving many Madurese to West Kalimantan to alleviate overpopulation on Madura. Since then, a number of conflicts have broken out between Madurese transmigrants and indigenous Dayaks. The Dayaks blame the Madurese for the loss of jobs and tribal land.

In 1999, ethnic Malays (who are predominantly Muslim, like the Madurese) clashed with the Madurese and enlisted the help of Dayaks (who are predominantly Christian). As a result, at least 200 Madurese were killed and some 35,000 fled to the provincial capital, Pontianak.

During 2000, the number of displaced Madurese in West Kalimantan increased by at least 20,000 because of the return to Pontianak of displaced Madurese who had briefly returned to Madura. Finding conditions on Madura unsuitable, and enticed by the government's offer of relocation, they re-entered the camps to await such relocation.

In October, a traffic accident in Pontianak involving a Madurese and a Malay reignited violence between the two groups. Ethnic Malays reportedly killed at least two Madurese in three days of violence. Indonesia put the displaced-persons camps under police protection and sent police reinforcements to halt the violence.

The displaced in Pontianak were housed in several "collective centers," including a football stadium (holding more than 10,000 persons), a Muslim pilgrimage center, a university stadium, and other large structures. Others sought shelter with family or friends. Local officials said resources were beginning to be strained and that the local community would not accept the displaced persons indefinitely.

In 1999 and 2000, the government relocated 500 displaced Madurese families to a settlement area some three hours from Pontianak by boat. Problems with the land at the new site, however, led many of the residents to question its long-term viability.

(In February 2001, violence erupted in Central Kalimantan Province as Dayaks began attacking ethnic Madurese. At least 500 persons, almost all Madurese, were killed and at least 50,000 Madurese were displaced in weeks of violence. The military evacuated most of the displaced to other parts of Indonesia).


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