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The Indonesian occupation of East Timor from 1975 until 2002 gave rise to a number of attacks on the Timorese civilian population, particularly against those suspected of being independence supporters.

The Accused, Jose Cardoso, was the Deputy Commander and subsequently the Commander of the pro-autonomy militia group Kaer Metin Merah Putih (KMMP). From May until September 1999, he issued a number of orders to attack both known and suspected independence supporters. These individuals were arrested, beaten and detained for months in cramped and extremely unhygienic conditions without regular access to food or water. One victim had his eat cut off and force fed to him on orders of the Accused. Two women were raped by the Accused. Two other individuals were murdered as a result of the Accused’s orders.

Cardoso was convicted for 9 counts of crimes against humanity by the Special Panels for Serious Crimes and sentenced to 12 years’ imprisonment.

Following the decision of the Indonesian government taken in early 1999 to offer East Timor the opportunity to vote for independence or for autonomy within the Republic of Indonesia, violence erupted in East Timor. The defendants in this case took part in a widespread or systematic attack directed against civilians that were in favour of an independent East Timor. One of the accused, Herman Sedyono, was the Bupati (District Administrator) of the Covalima District, one of the 13 districts in East Timor. As such, he was bearing the primary responsibility for maintaining peace and security in the region. Most of the other accused were Commander or just member of the Indonesian security authorities (TNI) or the Indonesian police force (POLRI), which were both promoting autonomy within the Republic of Indonesia.

In 1999, the Mahidi and the Laksaur pro-Indonesian militia groups, with the help of the TNI and POLRI, and with support from the Covalima District administration, repeatedly committed attacks against the Covalima population (mainly against those that were in favour of independence). The attacks involved crimes such as unlawful arrests, destruction of property, detention, and murder. The 16 accused were charged with encouraging, assisting and failing to stop, arrest or prosecute the perpetrators of the crimes.

Following violent clashes between two groups, one in favor of independence of East Timor and one against it, people of the former group sought refuge. In Liquiça, they hid in a church. In Diri, they hid in the house of one of their foremen. The attacks by an anti-independence militia caused the death and injury of many. It is claimed that several soldiers took part in the attacks. The question was whether the commander, Suratman, present in the area at time of both attacks, could be held responsible for what happened.

According to the Indonesian Ad Hoc Tribunal for East Timor, this could not be done. The involvement of his personnel could not be established and it considered the militia to be completely separate from the military. Thus, the Tribunal established that he had no effective control over those who actually committed the Crimes Against Humanity. The Tribunal could not conclude that Suratman had not taken enough action to prevent human rights violations from taking place. According to the Tribunal, he was there to look for a solution to the best of his abilities. Suratman was acquitted, which added to the international community’s concern about the effectiveness of the Tribunal.