The Indonesian Government has shown new signs of its determination to rid itself of East Timorese refugees, and thousands of them are now likely to be forced back across the border within the next three months.

The United Nations and the nascent government of East Timor have long wanted the estimated 50,000 to 80,000 refugees still in camps in West Timor to return.

Comments this week by Piet Tallo, Governor of Indonesia's East Nusa Tenggara province, which includes West Timor, suggest a pincer movement is now under way to get the refugees to return home.

Mr Tallo said on Wednesday that from January 1, daily food allowances and humanitarian assistance to the refugees will be stopped. He said all the refugee camps will be closed and only a few refugees will be allowed to settle in Indonesia.

This decision follows an Indonesian-run refugee registration process in June. Ninety-eight per cent of the refugees said then that they wanted to stay in Indonesia.

The impact of the process on the Jakarta Government was electric, UN sources said. "Jakarta threw its hands up in horror and said, 'Well, we don't want them'," said a source in Dili, East Timor.

The result frightened Jakarta into realising it was time to resolve a problem created by the Indonesian military-backed militias who rampaged through East Timor after its independence ballot on August 30, 1999, and forced about 250,000 East Timorese into West Timor.

But as the new administration prepares for its transition to full independence, the general feeling is that it is now time for the refugees, who have put enormous strain on Indonesia's resources, to return home. "The security of East Timor is no longer in question," a UN refugee administrator said.

Meanwhile, the UN High Commissioner for Refugees (UNHCR) has confirmed it will not be returning to West Timor. International agencies pulled out of West Timor after the murders of three UNHCR staff by a militia-led mob in West Timor in September last year. The UNHCR will now only help the refugees return to East Timor.

Although Indonesian government spokesmen have said plans are under way to resettle refugees in other parts of Indonesia, those close to the process claim Jakarta wants all refugees returned to East Timor. "It has taken two years, but the central Government in Jakarta is now very supportive of UN efforts to get the refugees back to East Timor," a UN source said.

The UN, and East Timor's president-in-waiting, Xanana Gusmao, have been actively seeking reconciliation with a handful of militia bosses – who still rule the refugees' lives. Several thousand refugees crossed back into East Timor last month after assurances were issued that the militia leaders would be safe there.

East Timor plans to set up a truth and reconciliation commission to heal the deep social rifts left by 25 years of political unrest and to promote national unity. The 40-member commission will be launched early next year and last for at least two years, project co-ordinator Pat Walsh said yesterday.