John Aglionby, Jakarta – A UN prosecutor and human rights groups called for international action yesterday after an Indonesian appeal court quashed the four outstanding convictions of members of the country's security forces prosecuted for their alleged involvement in violence in East Timor in 1999.

An international commission of experts appointed by the UN should assess the judicial processes in Jakarta and East Timor to bring the alleged perpetrators to justice, the human rights groups said.

It is estimated about 1,500 people were killed, 250,000 forcibly moved into Indonesian West Timor and almost all the territory's infrastructure destroyed during a UN-organised referendum in which the East Timorese voted to end Indonesia's 24-year occupation. The court's decision, made last month but confirmed yesterday, means of the 18 people indicted for crimes against humanity, only two, both East Timorese civilians, have had their convictions upheld.

Indonesian prosecutors could appeal to the supreme court but they are not expected to do so.

The serious crimes unit in East Timor, funded and staffed by the UN, has indicted 373 people. About 280 of these are at large in Indonesia including General Wiranto, the military chief at the time.

More than 50 members of the militias Jakarta created to disrupt the referendum and several East Timorese members of the Indonesian security forces have been convicted and jailed in East Timor.

Nicholas Koumjian, a UN-appointed prosecutor for serious crimes in East Timor, said Indonesia had failed to demonstrate its commitment to uphold human rights and the rule of law.

"The international community should now act to make sure impunity is not allowed to continue," he told the Guardian. "It should take a look at what happened and judge the process both in East Timor and Indonesia."

Amnesty International and Tapol, a campaign group for victims of alleged Indonesian oppression, said the UN should provide "meaningful justice for the victims".

Amnesty told the Guardian: "The trials and appeals in Indonesia have been flawed from the very start. The UN must ensure that its commitment to bring the perpetrators of human rights abuses to justice is fulfiled. Amnesty calls on the UN secretary general to set up an international commission of experts."

Paul Barber of Tapol called the decision a "travesty". "The UN, which has ultimate responsibility for justice must now evaluate the steps taken and consider alternative judicial mechanisms, including the establishment of an international tribunal for East Timor," he said.

Diplomats say an international commission, which is thought to have the support of Kofi Annan, the UN secretary general, is unlikely to be established, if at all, before Indonesia swears in its first directly elected president in late October.

East Timor's government is opposed to an international tribunal. In the interests of good neighbourly relations, it prefers to focus on reconciliation.

The four officers who have had their convictions overturned include the regional military commander at the time, Major General Adam Damiri. He has since played an important role in Jakarta's 15-month offensive against separatists in Aceh, northern Sumatra. Another officer, Colonel Noer Muis, is teaching an ethics course at the army's staff college.

Colonel Yani Basuki, a military spokesman, said the armed forces had not interfered in the judgment. "We respect the rule of law and let the judicial process take its course," he said. "Of course we think this was the correct verdict."

The judges also halved the 10-year sentence given to a militia leader Eurico Guterres. He and the former civilian governor, Abilio Soares, are the two East Timorese whose convictions were upheld.

The price of freedom

• Violence erupted in 1999, with Indonesian troops and militias blamed for deaths of approximately 1,500 civilians, forcing 250,000 people into Indonesian West Timor and destroying much of the region's infrastructure after East Timorese voted for independence
• Eighteen people indicted by Indonesia's tribunal into the violence.
• The most senior officer was Major General Adam Damiri. The defence minister, General Wiranto, and his immediate subordinates escaped prosecution.
• About half the indicted members of the security forces were convicted. All were freed on appeal. The two civilians who were tried, both East Timorese, were convicted
• Almost 400 people indicted by East Timor's UN-run tribunal. More than 50 were convicted, of whom about 280 are at large in Indonesia. An arrest warrant was issued for Gen Wiranto in May. Jakarta says it has done its utmost to deliver justice for the victims and the accused