But the refugees have not escaped the men who brought terror to East Timor. Our bodyguards tensed as we rounded a corner and came face to face with the militias who had laid waste to East Timor like an army from another age. They were coming across the border into West Timor with their families, and their belongings, wardrobes, motorbikes, dismantled huts. Nothing was too basic or too extravagant to take away - there was even a van with a satellite dish, so they could keep tabs on the nightmare they had created.
Lines of trucks waited at a barrier, some sprayed with the logos of militias such as the notorious Aitarak (Thorn). Women and children were crammed on board, clinging to the sides. The militia themselves were masked by balaclavas, or had bright scarves wrapped around their faces. "Don't talk to them," said one of the policemen escorting us. "They are angry. They might attack you."
The police made a show of confiscating a handful of clumsy, home-made guns. But minutes later, with the civilians deposited securely in a refugee camp, a truck headed back towards East Timor. The militia rode in the back with modern rifles and machine pistols, and a crate of beer.
Like the IRA with Northern Ireland or the Khmer Rouge with Cambodia, the Timorese militia are setting up bases on sympathetic territory outside their field of battle, well away from the mandate of the multinational peacekeeping force in the other half of the island.
The master-stroke has been moving their people with them. In the Atambua district alone, more than 100,000 have been brought over, doubling the population and, in effect, giving the militia control of the whole area.
"I just do what I'm told," said a market trader from the town of Maliana, where some of West Timor's worst recent atrocities are thought to have taken place as militiamen weeded out people thought to sympathise with the East Timorese independence movement. "I left because everyone was leaving. I don't care where I live as long as there's no fighting."
"Controlling the militia isn't easy," said Natsir Achmed, the local police chief. "In East Timor, they wore T-shirts identifying themselves. But over here they're mixed up with other armed forces and the refugees, and the situation is more complicated."
Once in Atambua, it becomes blindingly obvious that this is another element of the complex political and military process in East Timor which the United Nations has overlooked. From West Timor, the militia can run a highly effective guerrilla war against the multi-national force. They have supplies, weapons, sympathy and a population of supporters which they have moved into exile with them. The already tiny country will be, in effect, partitioned, with the peacekeepers unable to secure the western areas of East Timor.
Those suspected of war crimes in East Timor can live in Atambua without fear of arrest by Indonesian security forces and can travel freely from here. "We are victims of a war which began in 1975," said Herminio Davista da Costa, the chief of staff of the PPI, the umbrella organisation for all militia groups. "If we are bad, it is because the pro-independence fighters did bad things to us. Crimes have been committed by both sides."
"I don't know why people are talking about war crimes," said Adam Damiri, an Indonesian major-general whose military region included East Timor. "We were facing armed groups who threatened the lives of innocent people. We're asking the militia to lay down their weapons and if the UN lets us discuss things instead of accusing us of war crimes we could find a perfect solution."
Could Western governments and the UN have anticipated the slaughter that resulted when they backed an independence referendum in East Timor? On the remote island of Alor earlier last week, away from the tension in West Timor, I met a young member of the Aitarak militia. Enrique Lopez, 27, proudly wearing his black militia T-shirt, made a living organising card games and cock fights before taking up a machete against the UN. "A lot of us wanted to join the UN and help with the referendum," he said. "But the UN only took on people who supported independence. That's not fair, is it?"
Instead, the poorly educated, unsophisticated Mr Lopez joined the militia, and was told to hunt down pro-independence activists. It was all the same to him: he simply wanted to do something more with his life than work for a gambling syndicate. One wonders why the UN did not factor men like Mr Lopez into its East Timor plan. Instead, he was given the conditions in which he could commit the very atrocities the UN said it feared.
Earlier this year a senior British official confidently told me that East Timor would get its independence as scheduled. But the island could be faced with yet more decades of guerrilla war, with Atambua as the base, Mr Lopez still making his living as a fighter and the official moving on to tinker with a problem in another distant land.
n Humphrey Hawksley is a BBC World Affairs correspondent.Reuse content