Lindsay Murdoch – A pro-Jakarta militia leader has told investigators he helped murder an Indonesian journalist, two priests, two nuns and three other people in East Timor on the orders of a general in Jakarta.

The admission by John Marquez that unarmed civilians were killed on orders from Jakarta after the East Timor ballot on August 30 is the first to directly implicate the Indonesian military's top command in the atrocities.

An inquiry by Indonesia's Human Rights Commission has also taken evidence from an Indonesian policeman that he was ordered by a high-ranking Indonesian military officer to remove bodies from a church in the seaside town of Suai on September 6 and bury them 20 kilometres away across the border in Indonesian-ruled West Timor.

The bodies of 26 people, including three priests, were found in three graves and dug up early this week.

Mr Marquez was the leader of a militia group called Alfa which took part in killings after Indonesian Army officers gave him and other militiamen pills that made them violent, according to testimony obtained by investigators from the Jakarta-funded Human Rights Commission.

Church and human rights groups say they had heard that the Indonesian military gave drugs to militias to make them turn violent, but had no evidence.

Mr Marquez has told investigators the pills he and other militia received were to treat rabies, according to the Indonesian newspaper Kompas.

Investigators say Mr Marquez alleges that Indonesian soldiers pressured him to kill the journalist, Agus Mulyawan, who worked for a Japanese media company.

The killings happened near the town of Los Palos on September 25 when militia stopped a vehicle carrying Mr Mulyawan, the priests and nuns and three others five days after troops from the Australian-led Interfet landed in East Timor. At the time, the troops had not secured areas outside the capital, Dili.

Mr Marquez, who has been interrogated by Interfet troops and is in custody, did not name the general whom he said gave the kill order, investigators said.

All the people in the car were shot dead from close range. Commission investigators also revealed that another witness had testified that East Timor's former police chief, Colonel Timbul Silaen, ordered Indonesian police in the territory to take part in killings and destruction.

He has been promoted to Brigadier-General and now oversees corruption in Jakarta. He told the Herald last month that he was "doing the best for his country to uphold the law".

The Jakarta-based magazine Tempo names the former military chief of East Timor, then Colonel Tono Suratman, as one of the targets of the inquiry set up by Indonesia's former president Dr B.J. Habibie amid international outrage over the East Timor violence.

Tempo says the now Major-General Suratman's desk at military headquarters in Jakarta is full of files because he is "seriously preparing a defence". "Right now he's in a dangerous position," the magazine said. Appointed deputy armed forces spokesman, Major-General Suratman has refused repeated requests by the Herald to interview him.

Tempo also names the former military chief, General Wiranto, the former chief of the Bali-based Udayana command, Major-General Adam Damiri, former intelligence chief Major-General Zacky Anwar Makarim and Major-General Syafrie Syamsuddin as being among commissioned suspects in East Timor atrocities.

Major-General Syafrie and Major-General Zacky have key jobs at military headquarters reporting to the recently appointed military chief, Admiral Widodo.

Major-General Syafrie has denied allegations that he was present when militia attacked the Dili home of Bishop Carlos Belo, the head of the Catholic Church in East Timor.

The chief armed forces spokesman, Major-General Sudrajat, is quoted in Tempo denying that the named officers were guilty of any offence, claiming the commission's investigations were based on biased witnesses. "They are from the pro-independence side," he said.

But the commission secretary, Mr Albert Hasibuan, said the commission always gathered information from more than one witness.

Mr Hasibuan said if the commission's evidence showed Indonesian officers failed to order militia to stop the killing, "it's enough to take them to court". Since the ballot, Major-General Damiri has been promoted to operational assistant to the army's chief of staff. General Wiranto resigned as armed forces chief and was appointed Co-ordinating Minister for Political Affairs and Security in Indonesia's new Cabinet.

The United Nations has appointed its own five-member team to investigate atrocities in East Timor, expected to make its initial findings known within days.