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Actions by the government of Indonesia have been noted as a concern by advocates for human rights. Both Human Rights Watch and Amnesty International have criticised the government on multiple subjects. However, the country has had national human rights institutions, the National Commission on Human Rights (Komnas HAM) since 1993, which enjoys a degree of independence from government and holds UN accreditation.
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Reports from NGOs and the US Department of State
In its 2012 World Report, Human Rights Watch stated:
Over the past 13 years Indonesia has made great strides in becoming a stable, democratic country with a strong civil society and independent media. However, serious human rights concerns remain. While senior officials pay lip service to protecting human rights, they seem unwilling to take the steps necessary to ensure compliance by the security forces with international human rights and punishment for those responsible for abuses. This is opinion. In 2011 religious violence surged, particularly against Christians and Ahmadiyah, a group that considers itself Muslim but that some Muslims consider heretical. Violence continued to rack Papua and West Papua provinces, with few effective police investigations to hold perpetrators accountable.
Amnesty International, in its 2012 Report for Indonesia, stated:
Indonesia assumed the chair of ASEAN and in May was elected to the UN Human Rights Council for a third consecutive term. The government strengthened the national police commission but police accountability mechanisms remained inadequate. The security forces faced persistent allegations of human rights violations, including torture and other ill-treatment and use of unnecessary and excessive force. Provincial authorities in Aceh increasingly used caning as a judicial punishment. Peaceful political activities continued to be criminalized in Papua and Maluku. Religious minorities suffered discrimination, including intimidation and physical attacks. Barriers to sexual and reproductive rights continued to affect women and girls. No executions were reported.
The 2011 US Department of State Country Report on Human Rights Practices for Indonesia stated:
Indonesia is a multi-party democracy. In 2009 Susilo Bambang Yudhoyono was re-elected president in free and fair elections. Domestic and international observers judged the 2009 legislative elections free and fair as well. Security forces reported to civilian authorities.
Major human rights problems included instances of arbitrary and unlawful killings by security forces and others in Papua and West Papua provinces, societal abuse against certain minority religious groups, and abridgement of the rights of particular religious minorities to freely practice their religion by regional and local governments. Official corruption, including within the judiciary, was a major problem, although the Anti-corruption Commission (KPK) took some concrete steps to address this. Other human rights problems included: occasionally harsh prison conditions; some narrow and specific limitations on freedom of expression; trafficking in persons; child labour; and failure to enforce labour standards and worker rights. The government attempted to punish officials who committed abuses, but judicial sentencing often was not commensurate with the severity of offences, as was true in other types of crimes as well. Separatist guerillas in Papua killed members of the security forces in several attacks and injured others. Non-government actors engaged in politically related violence, including murder, in Aceh Province.
Torture and other ill-treatment
Security forces faced repeated allegations of torturing and otherwise ill-treating detainees, particularly peaceful political activists in areas with a history of independence movements such as Papua and Maluku. Independent investigations into such allegations were rare.
Caning was increasingly used as a form of judicial punishment in Aceh. At least 72 people were caned for various offences, including drinking alcohol, being alone with someone of the opposite sex who was not a marriage partner or relative (khalwat), and for gambling. The Acehnese authorities passed a series of by-laws governing the implementation of Sharia after the enactment of the province’s Special Autonomy Law in 2001.
Freedom of expression
The government continued to criminalise peaceful political expression in Maluku and Papua. At least 90 political activists were imprisoned for their peaceful political activities.
Some human rights activists and journalists continued to be intimidated and attacked because of their work.
Freedom of religion in Indonesia applies only to adherents of six major religious groupings, Buddhism, Catholicism, Confucianism, Hinduism, Islam and Protestantism. Questioning any of those six can lead to five years in prison for "insulting a major religion" and six more years if the Internet is used. .
Excessive use of force
The police used unnecessary and excessive force against demonstrators and protesters, especially in land dispute cases. In the rare instances where investigations took place, little progress was made in bringing perpetrators to justice.
Discrimination
Attacks and intimidation against religious minorities persisted. The Ahmadiyya community was increasingly targeted and at least four provinces issued new regional regulations restricting Ahmadiyya activities. By the end of the year, at least 18 Christian churches had been attacked or forced to close down. In many cases the police failed to adequately protect religious and other minority groups from such attacks.
Capital punishment
Indonesia's continuation of capital punishment, and the often corrupt judiciary and military has also led to political altercations with several human rights groups.
Police immunity
Amnesty International reports that over the last decade significant steps have been taken to reform the Indonesian National Police. The government has put in place legislative and structural reforms to strengthen their effectiveness in preventing and detecting crime, maintaining public order and promoting the rule of law. The police have also introduced internal regulations to ensure that international human rights standards are upheld during policing operations.
Despite these positive moves, credible reports of human rights violations committed by the police continue to emerge, with police routinely using unnecessary and excessive force and firearms to quell peaceful protests. Police have been implicated in beatings, shootings and killings of people during mass demonstrations, land disputes or even routine arrests.
Although the authorities have made some attempts to bring alleged perpetrators to justice using internal disciplinary mechanisms, criminal investigations into human rights violations by the police are all too rare, leaving many victims without access to justice and reparations.
This situation is made worse by the lack of an independent, effective, and impartial complaints mechanism which can deal with public complaints about police misconduct, including criminal offences involving human rights violations. While existing bodies such as the National Human Rights Commission (Komnas HAM) or the National Police Commission (Kompolnas) are able to receive and investigate complaints from the public, they are not empowered to refer these cases directly to the Public Prosecutor’s Office or to the police internal disciplinary body.
Domestic workers
In June, the President expressed support for the new ILO No. 189 Domestic Workers Convention. However, for a second successive year, parliament failed to debate and enact legislation providing legal protection for domestic workers. This left an estimated 2.6 million domestic workers – the vast majority of them women and girls – at continued risk of economic exploitation and physical, psychological and sexual violence.
Sexual and reproductive rights
Women and girls, especially those from poor and marginalised communities, were prevented from fully exercising their sexual and reproductive rights. Many continued to be denied the reproductive health services provided for in the 2009 Health Law, as the Ministry of Health had yet to issue the necessary implementing regulation. The government failed to challenge discriminatory attitudes and cruel, inhuman and degrading practices, including female genital mutilation and early marriages.
The maternal mortality ratio remained one of the highest in the region.
HR 2601 Section 1115
In 2005, the US Congress revised the previous fifty six year US policy of silence about human rights abuses in Indonesia, and on 28 July passed the US Congress 2006 Foreign Relations Authorization Bill H.R. 2601 which made specific mention of the ongoing genocide and legitimacy of its sovereignty of West Papua. Section 1115 was specific section referring to Indonesia and on 30 July 2005 the Jakarta Post reported:
President Susilo Bambang Yudhoyono warned the U.S. not to interfere in Indonesia's domestic affairs after the U.S. House of Representatives recently approved a bill that questions the status of Papua.
Although not mentioned in the US media, Section 1115 had become a leading Indonesian news story through August and September 2005. In the United States, the US Senate had since early 2001 been rejecting repeated efforts by the Bush administration to have US funding of the Indonesian military resumed, a ban which had been reluctantly imposed by the Clinton administration after TNI officers were filmed co-ordinating the Dili Scorched Earth campaign. By writing and passing Section 1115, the US Congress joins the Senate's earlier efforts to reduce, if not disengage, from the US fiscal and political support of the Indonesian military, a change of policy which brings both houses into conflict with the Bush administration and the executives of companies such as Bechtel.
Though Section 1115 states humanitarian and legal reasons for its existence, an additional factor would be security concerns due to ongoing employment of Al-Qaeda related terrorist militia by the Indonesian military and their continued funding programs for the Al Qaeda network. Given that the Senate opposition since 2003 has been strengthening on account of the TNI involvement in the death of Americans at the Timika mining site in 2002, the 2005 decision by Congress may reflect a desire to find more economical methods of cripling the Al Qaeda network.
Following President SBY's denouncement of Section 1115, Indonesian lobby groups such as The US Indonesia Society began renewed efforts to promote an Indonesian image of good management and renewed non-militant behaviour under General Susilo Bambang Yudhoyono's administration. SBY follows the administration of Megawati who in 2001 gave a public speech to the TNI instructing all members that they should disregard the issues of human rights in enforcing Indonesian unity and repressing any independence movements.
Papua and West Papua
International human rights organisations have criticised the Indonesian government's handling of protesters from the Free Papua Movement (OPM) in the Papua conflict, in which the OPM seeks the secession of Papua and West Papua. High profile prisoners from this movement include Filep Karma and Buchtar Tabuni, both of whom are considered to be prisoners of conscience by Amnesty International.
A report to the Indonesian Human Rights Network by the Allard K Lowenstein International Human Rights Clinic, Yale Law School alleges human rights violations in the region. The Indonesian military denies allegations of human rights abuses in Papua.
President of Indonesia Susilo Bambang Yudhoyono effected a policy change in 2005 away from "law and order" and towards economic development to arrest separatism in Papua. In May 2010, the release of Papuan political prisoners who had demonstrated for independence was announced. In October, a video emerged apparently showing soldiers kicking and abusing alleged separatists in Papua. The Government confirmed that the men were members of the military. The minister for security said their actions were excessive and unprofessional, and that they would be punished.
Additionally, there are reports of genocide by the Indonesian government. 100,000 Papuans are estimated to have been killed by the Indonesian government since 1963.