Persecution of religious minorities continued throughout 2009. Followers of the Ahmaddiya religious group faced attacks from Islamist groups that consider them heretics. On 11 December 2009, for example, a group of people claiming to be members of the Islamic Defenders Front (FPI) raided a house in Jakarta where Ahmadis had held Friday prayers, according to news reports compiled by the Wahid Institute, a Jakarta-based non-profit organization. Police took six Ahmadis to the police station in order to prevent them from being physically harmed, a police chief said. The deputy head of the FPI Jakarta chapter later said that his group had initiated the raid and demanded that police detain the Ahmadis for violating a government decree. A decree handed down in June 2008 does not ban Ahmaddiya outright, but it prevents Ahmadis, who number about 200,000 in Indonesia, from spreading their beliefs and orders them to embrace 'mainstream Islam', according to the Wahid Institute. Local governments issued bans against Ahmaddiya and other religious groups, including al-Qiyadah al-Islamiya, according to IRFR 2009. Twelve Ahmaddiya mosques were destroyed in 2009, including one in South Jakarta that was set on fire on 2 June.

In the province of Aceh, the Aceh Party gained a majority in the 9 April 2009 parliamentary elections. It then proceeded to implement elements of Sharia law that violate the human rights of women and members of non-Muslim minorities, according to local human rights groups. The party is the political wing of the Free Aceh Movement, which fought for independence before signing a peace agreement. During the run-up to elections, at least five Aceh Party leaders were killed, its offices were bombed, and Indonesian soldiers removed some of the party's flags, according to HRW. After winning the election, the Aceh Party formed a 'Sharia patrol unit' of 800 officers, which is tasked with forcing residents to adhere to the party's strict version of Islam.

Indonesia's Christian minority also continued to face attacks and discrimination. In January 2009, 10 members of Jemaah Islamiyah, a militant Islamic group, were tried for killing a Christian schoolteacher, according to IRFR 2009. In late October, at least 17 students from the Setia Christian College in Jakarta went on a hunger strike to protest the forced eviction of 900 students from their campus accommodation, an incident documented by AI. The students were housed in a building that was owned by the city, but was then turned over to a private company after a legal dispute. The previous year saw the evacuation of 1,400 students from the campus after attacks by villagers and others allegedly linked to the FPI, according to AI. Twelve churches were attacked and destroyed during 2009, according to IRFR 2009.

In resource-rich West Papua, authorities continued to clamp down, sometimes violently, on indigenous peoples' activists peacefully seeking greater autonomy or independence. Members of Papuan indigenous communities, who number 800,000, have accused the central government of exploiting the province's natural resources, which include mineral deposits and forests, without compensating them. They have also raised concerns about non-Papuan migration into the province. On 29 January 2009, police in Nabire fired rubber bullets and injured at least five people who were demonstrating for local elections to be held, according to AI, which reported that police also beat demonstrators with rattan sticks and rifle butts. In January 2009, Papua's High Court extended the sentences of 11 protesters who were jailed after raising the banned Morning Star flag, a symbol of independence, in March 2008. The protesters were initially sentenced to eight months' imprisonment, but upon appeal the sentences were extended to three and a half years for one protester and three years for the others. On 6 April, police opened fire on students peacefully protesting the elections and calling on the UN to organize a referendum to determine the future of Papua. Four demonstrators were seriously injured, including a 10-year-old boy. Three days earlier, police arrested 20 student demonstrators and charged three with treason and incitement, charges that carry a maximum penalty of life imprisonment. These incidents were documented by HRW. In June 2009, HRW released a report documenting abuses by the Indonesian Special Forces, Kopassus, in West Papua. Drawing on interviews collected from victims in 2008 and 2009, HRW said Kopassus members 'arrest Papuans without legal authority, and beat and mistreat those they take back to their barracks'. The report noted that Australia has resumed regular training of Kopassus soldiers and pointed to statements by US Secretary of State Hillary Clinton that suggest that the US may also decide to train Indonesian Special Forces. On 11 August 2009, AI released a statement decrying the failure to resolve the killing of Papuan protester Opinus Tabuni one year earlier. According to AI, the unsolved murder 'highlights the continued lack of accountability in cases involving the lethal use of firearms by law enforcement officials'.

In 2009, Indonesia set up a legal framework to implement a UN-backed programme to reduce greenhouse gas emissions through market incentives. After China and the US, Indonesia is the world's largest emitter of greenhouses gases, mostly due to rampant deforestation, according to the World Bank. Logging – both legal and illegal – as well as mining and conversion of forested areas to palm oil plantations, are responsible for most of the massive deforestation, which threatens not only the environment, but also indigenous communities. The Reducing Emissions from Deforestation and Forest Degradation (REDD) programme would see big polluters buying carbon credits, generating financial resources that would be used to pay for reforestation or forest preservation. Under the REDD programme, the Indonesian government plans to plant millions of hectares of new forest annually with financing from international donors and the private sector. Some indigenous communities, including Oma'lung, a subgroup of Dayaks living in Borneo, have reportedly embraced the REDD programme as a path to preserving their homeland and culture, according to Our World 2.0, a publication by the United Nations University, which is a think-tank for the UN. Nevertheless, the Indonesian government must ensure proper and meaningful consultation with affected indigenous communities and ensure that no forced displacement occurs in conjunction with any REDD programme.

This is not a UNHCR publication. UNHCR is not responsible for, nor does it necessarily endorse, its content. Any views expressed are solely those of the author or publisher and do not necessarily reflect those of UNHCR, the United Nations or its Member States.