Nature has taken over the garden of Manuel Carrascalao's house in Dili. Tall weeds grow between paving stones and flies buzz in the air. As you approach the well at the back of the garden, the soft hum of millions of maggots becomes audible.

Inside the well, clearly visible under the moving mass of white maggots, is the decapitated body of a woman, her torso rising up and legs bent to one side. The stench of decomposing flesh is overwhelming.

There may be many more bodies under that of the woman; the well is usually 20 metres deep and her body lies only half a metre from the surface. But, at first glance, it is impossible to tell.

It was in April that Mr Carrascalao's house first became the focus of militia violence. The leading pro-independence figure had been sheltering some 200 refugees in his house and grounds.

On April 17, Aitarak militia led by Eurico Guterres attacked, shooting and threatening refugees and the Carrascalao family with machetes. The official death toll from that day is 13, including Mr Carrascalao's 18-year-old son. But the unofficial toll may be as high as 60.

Since the attack, the house has been deserted. Papers, photographs, clothing and the personal effects of the family that fled litter the floor among smashed glass and broken furniture.

A few weeks ago the house became the centre of activity – not as a family home where visitors were entertained and children played – but for something far more sinister.

Three meat hooks hanging from the walls of one of the outhouses suggest that this house had become a place of torture and murder.

"People were hanged from meat hooks, with cloth around their necks. They were killed here," said Domingos Xavier, who appeared in the garden with some young boys. He had arrived to make sure we had seen the body.

Mr Domingos said Aitarak militia and Indonesian soldiers were responsible for the killings. He did not say why the people had died, but he believed it must have been because they supported independence.

He said they were killed in the outhouses and then dumped in the well. "There are many bodies there on top of each other. It is impossible to say how many. They have been here two weeks," he said, his hand over his nose to lessen the smell.

Two doors down, at the Hotel Tropical, is the headquarters of Aitarak itself. The stench of decomposing flesh lingers here too, along with the smell of rubbish and food collecting behind the hotel rooms.

Australian troops came here yesterday and removed weapons. An empty box of Russian ammunition lies in the courtyard among discarded blue pro-autonomy baseball caps. "Aitarak has been gone for a week," said Mr Domingos, who led us through the mass of rooms and courtyards.

Among the empty cans of baby milk and beer bottles, photographs lay on the floor. One of them shows a group of young men tending graves in the Indonesian heroes' cemetery, where soldiers killed during their tour of duty in East Timor are buried.

There have been many reports over the past few weeks of mass killings in East Timor during the reign of violence and terror by the militias and Indonesian armed forces.

Although there is anecdotal evidence to suggest many people were targeted and killed, there is, as yet, no hard factual evidence to prove systematic slaughter.

At police headquarters in Dili, there is nothing to suggest the mass of bodies stored in detention cells which Australian aid worker Isa Bradbridge and his wife reported two weeks ago.

Now deserted, apart from seven officers, and destroyed by the soldiers who patrol out in front, there is no sign of blood and no sign of a clean-up.

According to police chief Lieutenant-Colonel Sitompul, the reports are false. He gave a tour of the headquarters to prove it. "See for yourself. There are no bodies here," he said. He showed two empty coffins in a large hall.

"Four boxes were prepared for personnel and two were used, maybe the witnesses mistook this," he said. But the house of Mr Carrascalao is one place where there is evidence that killing and possibly organised torture has occurred.

By late afternoon yesterday Interfet peacekeeping troops had pulled eight bodies from the well.