The disquiet was shared by many aid agencies, who have reported that thousands of the refugees may be incarcerated in camps guarded by militiamen in the border town of Atambua and also around the West Timorese capital, Kupang. Meanwhile, militia leaders boasted yesterday that they would not lay down their arms. It was also reported by the government in Jakarta that the militia still number 50,000.
Many of those militiamen are believed to be in West Timor. The concern about their presence was relayed yesterday by the UN High Commissioner for Refugees, Sadako Ogata, to President B J Habibie at a meeting in Jakarta. Officials said she pressed him to guarantee access to the camps for humanitarian workers.
To what extent the Indonesian authorities are in control in West Timor, however, was still not clear. Mrs Ogata traveled to the province on Sunday but was allowed to visit the Atambua camp for only an hour. She was prevented from approaching any of the refugees. "She was not allowed to talk to them or inquire as to the conditions. It was, shall we say, a diplomatic visit," Mrs Ogata's spokesman said.
UN officials are concerned that the refugees may have become the hostages of the militia who mean to use them later to try one more time to thwart the independence process in East Timor.
"In the refugee camps in West Timor, there are also militia and they are terrorising people," John Sayer, Hong Kong director of Oxfam, said yesterday. "They are going through people who are either on the road or have reached the camps, looking for supporters of independence, young people who maybe have been active in the independence vote, singling people out and taking people away.
"Our big worry is that even with the peace-keeping force coming back in, the resettlement of people from West Timor - which is still controlled by the Indonesian authorities, predominantly the military, but still has a very large militia presence - will those people be able to return to East Timor? That is still a big question."
What is happening in West Timor and perhaps also in several other parts of Indonesia affected by influxes of refugees - for example Irian Jaya, the island of Flores and even Lombok, close to Bali - graphically illustrates the limits of the peace-keeping operation now under way.
The foreign troops are not authorised to cross into West Timor, which remains Indonesian soil. They are being asked to usher in a new era of independence and liberty for a province that is missing as much as one- quarter of its people. "Militias who had operated in East Timor are perpetuating terror in West Timor," the executive director of the Australian Council for Overseas Aid, Janet Hunt, said yesterday. "Accounts from reliable sources say that militias are searching for independence supporters and have been seen taking men and boys from camps."
Meanwhile, President Habibie is likely to face tough questions from sceptical Indonesian MPs today on why he let foreign troops flood into East Timor. The strength of the militia was spelled out yesterday by Major-General Sudrajat, the chief spokesman for the Indonesia army. He told reporters that Eurico Guterres, the head of the feared Aitarak (Thorn) militia and deputy commander of all the militias, had said he had 50,000 men.
Basilio Araujo, a spokesman for the National United Front, a new umbrella organisation for the militias formed at a rally inside West Timor on Sunday, warned that they would not lay down their arms and would fight to "free East Timor from the new colonialists". He added: "We know better our countryside, where to hide and how to avoid malaria mosquitoes. Let the UN troops die of malaria disease."
The chief of the Indonesian army, General Wiranto, insisted that fewer than 100 had died in the violence. "The number of victims that we have recorded since the announcement of the result of the referendum is roughly in the 90s," General Wiranto said. "That is the number that we have recorded so far. It is not the tens of thousands or hundreds of thousands as reported by the foreign media."