Sian Powell, Dili – The pro-Jakarta militia in East Timor conducted a concerted two-stage campaign to split up families, warning men they would be killed if they did not flee, then forcibly transporting the remaining women and children to West Timor.

Sidney Jones, the Asia director of Human Rights Watch, who has interviewed hundreds of returned refugees in East Timor, said it was a comprehensive pattern of dislocation, which continued in the camps in West Timor.

"Women were told their husbands had been killed and there was no point in going back, their villages had been destroyed, that Interfet soldiers would rape them," she said.

The villagers were usually transported to the district military command before being forced over the border and Ms Jones has documented three cases of rape in these commands in Suai, in the south of the territory.

"There is no question TNI (the Indonesian army) was involved, and active-duty officers were actually in the militia, particularly in the western regions," she said.

These soldiers were also East Timorese and many other East Timorese, of the Tentara Tiga Bulan – literally the three-month army, a reservist force – were also involved.

Apart from the already documented massacres, such as the killings in the church in Suai, where an estimated 200 people were shot dead, and the deaths by stabbing of 47 people in the police station in the border town of Maliana, Ms Jones said her understanding was that most killings were more targeted.

"My guess is that [the deaths] will add up to several hundreds," she said. "The determination was to push everybody out across the border." There were two reasons for this, she said.

First, the militia and the TNI wanted to convince the world that the UNAMET ballot was rigged and that East Timorese were so averse to independence they had fled in their thousands. Secondly, they wanted to clear the territory of independence activists and sympathisers to aid the return of the militia.

From her interviews, Ms Jones learned that members of Kopassus, the Indonesian special forces, arrived in Dili in the week before the ballot and fanned out across East Timor.

Of equal concern, Ms Jones said, was evidence that militia members were often very young. She had been told of one boy of 10 who was a militia member and others of 14, 15 and 16. Contrary to common perception, they were nearly always East Timorese and known to their victims, sometimes even related to them.

Ms Jones said there was still a great deal of investigative work to be done before the whole truth about the devastation of East Timor emerged. "There is still a lot we don't know," she said, "there's still a lot that has to be followed up."