Louise Williams, Jakarta – As the Indonesian military faces a damning human rights investigation, residents of the northern province of Aceh are guarding what are claimed to be mass graves, saying they fear there will be attempts to remove the evidence.

Indonesian troops began withdrawing from Aceh yesterday, following a public apology to the province's people by the armed forces chief, General Wiranto, for human rights abuses.

General Wiranto ordered the withdrawal after local human rights groups identified mass graves believed to hold the remains of thousands of victims of torture and summary executions during military operations between 1989 and 1992, and again from last year until June. "There are signs of the killing fields," a diplomatic source said. "There were people disappearing, people being killed, rapes, brutality and lack of discipline on the part of the military forces in the area."

A representative of the Legal Aid Institute in the provincial capital of Banda Aceh said six bodies had been dumped in the city recently with signs of torture, following the public statements about military abuses. "We believe there is a movement to scrap the evidence, and we suspect some people are trying to dig up the graves and remove the bones," he said. "Local people are taking turns to guard the site."

The Indonesian Commission on Human Rights was due to send a fact-finding team to the sites late yesterday, saying the human rights violations in Aceh, East Timor and Irian Jaya were systematic and typical of the regime of the former president, Mr Soeharto.

The first 250 troops were due to leave yesterday, and another 800 at the end of the month. The military authorities have not revealed how many troops will remain. "The Indonesian armed forces is fighting to save its image," the diplomatic source said. "An investigation into the Aceh killings will be difficult to quarantine because it implicates a lot of senior officers who are still in top positions."

While there have been some leadership changes in the armed forces since Mr Soeharto stepped down in May, many of the most senior generals remain in powerful positions either in the military or the Government of Dr B.J.Habibie. The military is also facing investigations into the kidnapping and torture of democracy activists and the shooting of student protesters under Mr Soeharto.

The military offensive in Aceh began in 1989 to put down a fundamentalist Muslim movement fighting for an Islamic state in the mainly Muslim province. Local grievances were fanned by economic injustice as the people of Aceh watched their valuable gas and oil resources being skimmed off by Jakarta and multinational companies with few benefits returning to the province.

At its height the Aceh Merdeka (Free Aceh) movement numbered up to 1,000 followers, but estimates now put the force at no more than 30 poorly organised guerillas confined to the jungles. The military operation against Aceh Merdeka targeted suspected sympathisers as well as guerillas, and according to Amnesty International 2,000 people were killed between 1989 and 1992, and another 1,600 disappeared.

During national elections last year the campaign of fear and brutality was stepped up again to ensure support for the ruling Golkar party, according to diplomatic sources. "There is a great deal of trauma and fear in Aceh," a source said. "Widows of men who were killed were even ostracised because people feared they would be taken as well if they associated with the surviving family members."

The Jakarta Post reported: "Estimates made by independent investigators on the basis of field observations and interviews indicate the number of people who were killed, went missing or were physically abused runs into thousands."