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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.

The Accused, Laurent Semanza, was the former Bourgmestre (mayor) of Bicumbi commune. He was indicted on 14 counts of genocide, crimes against humanity and war crimes for his role in the Rwandan genocide.

On 15 May 2003, Trial Chamber III of the ICTR found him guilty of aiding and abetting genocide during the massacres at Musha Church and Mwulire Hill, which took place on 13 April 1994 and 18 April 1994 respectively. The Chamber also convicted him of extermination as a crime against humanity for his conduct at Musha church and Mwulire Hill. The Trial Chamber further held that Semanza was guilty of torture and murder as crimes against humanity. These convictions arose out of Semanza’s April 1994 incitement of a crowd in Gikoro commune to rape Tutsi women before killing them. He was also held directly responsible for the torture and murder of Rusanganwa, a Tutsi, whom he attacked and killed during the Musha Church massacre.

However, the judgment acquitted the Accused of genocide, direct and public incitement to commit genocide, serious violations of Common Article 3 and Additional Protocol II of the Geneva Conventions, and persecution as a crime against humanity.

The Trial Chamber sentenced the Accused to 25 years of imprisonment. This sentence was reduced by 6 months because of violations of the Accused’s rights that occurred while in detention prior to his transfer to the ICTR.