Rajiv Chandrasekaran, Suai – Scores of 7.62mm shell casings litter Father Francisco's bedroom floor. At least 60 bullet holes pockmark the bamboo-scaffolded facade of Ave Maria Cathedral. A thick coating of dried blood stretches across the entrance to a church schoolroom. A pile of underwear sits at the foot of a staircase.

It was here on September 6, at a Roman Catholic compound comprising the cathedral, Our Lady of Fatima Church and several other buildings, that survivors say a throng of pro-Indonesia militiamen engaged in one of the bloodiest acts of retribution against the people of East Timor, who days earlier had voted to secede from Indonesia.

Armed with assault rifles, machetes and hand grenades, the militia members set upon independence supporters inside the compound, raping dozens of women and slaughtering more than 100 people, including three priests, according to the survivors.

Their account of what happened, the first provided by witnesses, is similar to that of a nun, Sister Mary Barudero, who described the incident to a reporter at a refugee camp in the western Timor city of Kupang last month. Her description – relayed from another nun who was in the compound at the time – and a report by the Vatican missionary news service Fides served as the basis of a story in The Washington Post on September 11.

But despite all the indications of a mass killing here, Australian army investigators with an international peacekeeping force have run into an unusual hurdle in trying to determine exactly what happened – a lack of bodies.

Thus far, the investigators have found only two sets of human remains in the torched and looted compound. They believe, based on reports from survivors of the attack and other witnesses, that the militiamen disposed of the bodies by burning them near the church, loading the charred corpses on a truck and then dumping them in one of several crocodile-filled lakes on the outskirts of Suai, a coastal town about 60 miles southwest of Dili, the East Timor capital.

Human rights officials contend that militia groups took similar care to conceal other large-scale killings in East Timor, which they fear could hinder efforts to apprehend and prosecute those responsible.

In the central town of Maliana, for instance, the bodies of 47 people allegedly hacked to death with machetes were carted to the coast, placed on a boat, weighted down with sandbags and tossed into the sea, the officials said. As of Wednesday, only three bodies had washed ashore.

"The great lengths the militias have gone to to hide and destroy the bodies makes it very difficult for us to figure out what happened," said Capt. Jens Streit, an Australian army lawyer who is investigating human rights violations as part of the Australian-led multinational peacekeeping mission. "We have eyewitness accounts, but other than things like shell casings and blood stains, we don't have a lot of physical evidence."

Peacekeeping and human rights officials do not have an estimate of the number of people killed in the rampage, but they believe that large-scale killings, such as the one alleged in Suai, were rare. More common, they say, were attacks that killed fewer than 10 victims. Around Dili, for example, investigators have found 20 sites at which they believe people were killed in militia violence, but no more than nine bodies were found at each location.

But even in those cases, officials said, the killers took steps to cover their tracks, particularly by burning corpses. "In Kosovo, they didn't care about what the world saw," Streit said. "The Indonesians are extremely concerned about saving face. They want to be able to deny any of this happened."

UN human rights commissioner Mary Robinson has appointed a five-member commission to look into the East Timor violence, but as of today no UN investigators have entered the country. A UN spokesman said they are waiting for security conditions here to improve.

In the interim, the task of gathering evidence has fallen to Australian army lawyers and military police, who have been scouring the Suai church for clues before they are pocketed by local residents or washed away by rain. Military police also have been talking to witnesses.

One, Eliziu Gusmao, recalled the afternoon of September 6 as a barrage of almost indescribable violence and hours of sheer terror. Gusmao, a nurse who had lived in a town near Suai and who is no relation to the East Timorese independence leader with the same surname, said he moved into the church compound with his family in May after being threatened by a local militia group. He said he was singled out because he was involved with the National Council for Timorese Resistance, a pro-independence group.

Because they offered such refuge and because Roman Catholic clergy often were identified with the independence movement – mounted against largely Muslim Indonesian authorities – Catholic institutions and churchmen were frequent targets of attacks by the pro-Indonesian militiamen.

For months, Gusmao, his wife and their 3-year-old son lived in a tent pitched on the spacious compound, between the cathedral, which is still under construction, and the church. In the weeks leading up to the August 30 independence referendum, he said, hundreds of other pro-independence families fearful of the militia groups also took refuge on church property. On the morning of September 6, Gusmao said, several hundred militia members gathered on the street outside the compound, so he and his family decided to hide near the convent, which was far from the street and directly across from the church. Their peace of mind did not last long. By 2pm, the militiamen had scaled the fence and surrounded the church.

At 2.30, Father Dewanto walked out the front door of the church to try to talk to the militiamen, Gusmao said. Within seconds, a machete-wielding man charged at him, chopping at the priest's arm and neck. Moments later, Father Francisco came out the door. This time, the militiamen responded with gunfire, cutting him down on the church steps.

"Then one of the militiamen shouted, 'Father Hilario is in there. Let's go in there and shoot him,'" Gusmao said. When Father Hilario, the senior parish priest, did not heed the militiamen's shouts to come outside, a small group ran up the left side of the church and entered his study. A burst of automatic-weapons fire followed. A few seconds later, Father Hilario walked into the courtyard and collapsed, his white robe turning red, Gusmao said.

He said the order to kill Father Hilario was given by Izidio Manek, a local militia leader. Gusmao also said he saw several uniformed Indonesian soldiers at the church. The 7.62mm rounds found in the church are used in several types of military weapons.

Gusmao then ran to his family, which was waiting at the convent, and told them to flee. They ran out toward the street, where he believes they were put on a truck by militiamen and taken to a camp in Indonesian-controlled western Timor. He has not heard from them since.

Gusmao, however, decided to stay behind, climbing into a drainage ditch next to the convent, where he covered himself with leaves. For hours, he said, "it sounded like a war."

"I heard people screaming, people crying, people shouting," Gusmao said in a lengthy interview at the church compound. Pointing at the convent, he said, "They were even pulling women away from there." At 11pm, after the noise subsided, Gusmao said he crawled out of the ditch and walked around the convent toward a row of school rooms. As he walked by one, he saw "a huge pool of blood inside." Then, as he proceeded toward the church, he saw the carnage. "There were more than 20 bodies piled in front of the church," he said. "Some had been shot. Some had their arms chopped off. Some had their heads chopped off. It was awful. I was not sure if they were dead or not, so I nudged them with my foot. But they were dead. All of them."

Gusmao said he quickly knelt and prayed, asking God to "receive their souls in heaven." Then he ran into the hills that surround Suai, where he remained in hiding for more than a month, he said, subsisting on river water, bananas and cassava plants, returning only when he received word that the peacekeepers had arrived.

The chronology related by Gusmao matched that of 13-year-old Atanacio de Costa Martinez, Father Hilario's nephew, who said he was in the church – hiding under Father Francisco's bed – during the shooting rampage. After Father Hilario was killed, Atanacio said the militia members entered the church and sprayed people inside – mostly women and children – with gunfire.

When the militiamen set fire to the church, Atanacio said, he jumped through the window of Father Francisco's room and sprinted out the rear of the compound. As he was leaving, he said he saw two large piles of corpses behind the church.

"There were dozens of bodies," Atanacio said. "They had been shot. They had been stabbed."

While he was in the ditch, Gusmao said he heard a militia member ride up on a motorcycle and shout at his colleagues, 'Where are the trucks? We want to bury the bodies.'"

Gusmao, a shy man who repeatedly appeared on the verge of sobbing as he recounted the incident, said one of his instincts as a nurse prodded him when he reached his hiding place in the hills at 4am. He took out a small red notebook and jotted down his memories of the killings. Later, he complied a list of 36 local militia members and soldiers, many of whom he believes were involved in the attack.

"There is much pain in my heart," Gusmao said as he walked away from the compound, toward his new job at a emergency medical clinic set up by French volunteers. "I am sad not just for the victims, but for those who were from East Timor who conducted this against their own people."