Discrimination, harassment and violence against religious minorities in Indonesia increased in 2011. The Setara Institute, an Indonesia religious rights monitoring organization, recorded 244 such incidents, up from around 200 the previous year; government officials, military and police were responsible for many of the incidents.

Ahmadiyya Muslims continued to be one of the main targets for violence and abuse. Three Ahmadis were killed in February in West Java, after a group of 1,500 people attacked 21 of them, in order to expel them from the village. Police did little to intervene. Twelve men were tried, and received sentences of between only three and six months, on a variety of charges but not for manslaughter.

By September, 26 regencies and municipalities across the country had issued decrees banning or restricting Ahmadiyya religious practice, stemming from a 2008 ministerial decree preventing public propagation of the Ahmadiyya faith. The decree contradicts President Susilo Bambang Yudhoyono's continual assertion of Indonesian 'tolerance', and is justified on the logic that restricting the religious expression of minorities serves to protect them from violence.

The government continues to push the Religious Tolerance Bill, but rights groups have denounced the draft bill, completed in October, for limiting certain activities in the name of tolerance. For example, the bill attempts to regulate proselytizing, celebration of religious holidays, construction of houses of worship, holding of funerals and organization of religious education. The bill continues to define and punish blasphemy; existing laws on blasphemy have already served to discriminate against and harass religious minorities.

Indigenous peoples have long struggled to realize their rights in the Indonesia state, especially the right to land and free, prior and informed consent. In May, as part of the government's agreement with Norway over the Reducing Emissions from Deforestation and Forest Degradation (REDD+) project – a US$ 1 billion project to protect forests and reduce carbon emissions while fostering economic development – President Yudhoyono, declared a two-year moratorium on new concessions in primary forest and peat lands. But this was flouted: ongoing illegal clearing of these protected lands in Central Kalimantan by a Malaysian company was reported by Indonesian NGOs.

In December, the Indonesian parliament passed a new bill which will allow the government to acquire land from citizens in the name of a vaguely defined 'public interest'. The legislation is intended to settle disagreements over evictions and speed up infrastructure projects. Those affected do not have the right to appeal and compensation is only provided upon proof of certification of land-ownership, often lacking in the case of indigenous communities. A coalition of Indonesian NGOs says the bill is a direct threat to the rights of indigenous peoples and is likely to increase conflict over land.

Indigenous communities struggling to secure their right to land won a small victory in September, as two articles of the 2004 Plantation Act were dropped after being declared unconstitutional by the Constitutional Court for discriminating against indigenous farmers. The articles, which prohibited damaging plantation land or equipment, or preventing plantation business have been used to imprison and fine hundreds of people who have protested against corporate grabs of ancestral lands, especially by palm oil companies.

However, in October, the Indonesian government curtailed the legitimate activities of rights defenders by passing the long-debated Intelligence Bill – giving law enforcement power to spy on civilians to protect 'national security'. Military documents exposed by HRW in 2011 suggest that unlawful military spying on peaceful activists in Papua is commonplace.

In Papua, the government failed to make any progress towards implementing the rights granted to the province under the Special Autonomy Law of 2001. At least three people were killed in October by security forces during the Third Papuan People's Congress, a peaceful gathering of indigenous Papuans demanding a referendum on independence from the Indonesian state. Security forces have yet to be held accountable. Six indigenous Papuan men were charged with treason, adding to the approximately 40 existing Papuan political prisoners, according to the AHRC. Cases of torture, arbitrary detention and military operations continued to be reported during 2011 in the provinces of Papua and West Papua.

Indonesian military and special police forces conducted massive counter-insurgency 'sweeping' operations aimed at suspected Free Papua Organization (OPM) separatists in the central highland area of Panai, West Papua. The Jakarta Post reported that at least 500 people had fled from Dagouto village since raids in November. Local media estimate the military operation has forced about 10,000 people to flee their villages, and that 20 villagers had been shot. The raids had been escalating since April. Indonesia's National Commission on Human Rights (Komnas HAM) called on the National Police chief to withdraw all troops from the area.

In 2011, police admitted to receiving pay-offs from the US-owned Freeport-McMoRan to protect their Grasberg gold and copper mine in Papua, the largest gold mine and third largest copper mine in the world. This mine project has long been criticized for violating the rights of indigenous Papuans through land confiscation, environmental destruction and militarization. Indonesian military forces who 'protect' the mine have reportedly raped Papuan indigenous women.

Papua has consistently had the highest rate of HIV infection in Indonesia, at 15 times the national average. In May, the head of the Papuan AIDS Prevention Commission reported that the number of people living with HIV/AIDS in Papua jumped by 30 per cent in four months, to over 17,000. Mimika, the district of Freeport McMoRan's mine, had the highest increase and overall number of HIV/AIDS-infected people, with associated high numbers of prostitutes and brothels. While these numbers do not differentiate, past studies have suggested that prevalence of HIV/AIDS among Papuans is twice as high as among non-Papuans.

The rights of indigenous Papuans to their ancestral lands also continued to be threatened by the Merauke Integration Food and Energy Project (MIFEE), a mega-agro initiative launched in 2010, which involves the conversion of a vast area of land, including forests, into plantations. In a report submitted to various UN mechanisms in 2011, an NGO coalition claims that MIFEE has proceeded without regard for the principles of free, prior and informed consent, and has forcibly acquired around 2 million hectares of traditional lands. The military has also reportedly been harassing those resisting the project. In October 2011, President Yudhoyono set up the Unit for the Acceleration of Development in Papua and West Papau (UP4B) to stimulate economic development. Little attention has been given to Papuans' right to autonomy and self-governance, however.

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