Excavations in the province of Aceh, in northern Sumatra, found at least 24 sets of remains, apparently victims of the Indonesian military's attempt to wipe out a Muslim independence movement in the late 1980s and early 1990s.
Some of the skulls contained bullet holes, and there were traces of ropes which had been used to bind the victims before they were shot.
"After digging at these sites today, I believe that what the Acehnese people say about killings in the province is true," said Baharuddin Lopa, head of Indonesia's official National Commission on Human Rights yesterday. "This proves Aceh has been a killing field."
Mr Lopa's investigators returned to the Indonesian capital Jakarta last night after a three-day investigation during which they visited several sites. Local people believe the graves of some 1,600 people may lie there.
The sites included a beach, waste land, and a house said by locals to have been used by the military as a torture centre. Traces of two bodies, including finger bones, were discovered near the building but locals said that many more bodies had been removed by the military before it abandoned the building last week.
In the three months since the resignation of President Suharto, the Indonesian armed forces (Abri) have been put on the defensive by mounting evidence of the brutal role they played in supporting his 33-year dictatorship.
In an unprecedented admission last Friday, the Abri commander, General Wiranto, admitted the possibility of "excesses" during military operations in the provinces of Aceh, East Timor and Irian Jaya, and acknowledged that army units had been involved in the abduction and torture of democracy activists, and the devastating riots which raged through Jakarta in mid-May.
"Abri is aware that in the above incidents, troops were involved," he said. "We are determined to review the military's institutional ethics and leadership so that such violations of procedures do not happen again."
Earlier this month, General Wiranto travelled to Aceh to apologise in person for past abuses and to announce the removal of combat units which were jeered and booed as they began their withdrawal last week.
Small numbers of Muslim insurgents are said to live still in the remote mountains of Aceh but in the early 1990s their activities were effectively curtailed by a brutal military campaign which killed unarmed civilian sympathisers as well as thousands of the guerrillas themselves.
The National Commission on Human Rights says that it has heard testimony from Acehnese women whose sons and husbands mysteriously disappeared in the province as recently as this May.
Many active rebels have fled over the years to Malaysia where abductions were also reported this year, allegedly under an agreement between the Indonesian and Malaysian authorities.
Mr Lopa's team will soon visit the Sumatran province of Lampung, where separatist activity was met with similar brutality during the 1980s.
President Suharto's successor and former protege, BJ Habibie, has done away with much of the repressive apparatus of the old regime, but remains opposed to independence for any of the regions claimed by Indonesia.Reuse content