In the Balinese capital, Denpaser, hundreds of fugitive East Timorese went into hiding after soldiers and militiamen picketed banks, shops and phone offices, barring refugees and threatening to kill them.
Last week Indonesian soldiers fired into the air near where refugees were staying. Local authorities say the arrivals are infected with malaria and several hotels in Bali have been ordered to report East Timorese guests to the military.
Militia members have been seen carrying lists bearing the names of those associated with the independence movement, including political activists, students, humanitarian workers, nuns and Catholic priests.
Reports by human rights organisations suggest that dozens of people appearing on such lists were murdered in mid-September as they evacuated East Timor by boat, and their bodies dumped in the sea.
The UN High Commissioner for Refugees and the National Council for East Timorese Independence are trying to evacuate as many as 2,000 East Timorese trapped in Indonesia, but the plan is foundering.
Many refugees are reluctant to disclose their names and locations to the humanitarian agencies, fearing the lists will be passed to the Indonesian government. There is also the problem of where the refugees will go after leaving Indonesia.
"We are very worried for the security of East Timorese in Indonesia, especially as they make their way from safe houses to ports and airports," said a spokesman for Amnesty International. "They are refugees and they should have the same rights and protection as refugees anywhere."
Earlier this month Australia received more than a thousand refugees who had taken refuge in the United Nations compound in Dili, but Canberra is said to be reluctant to accept sole responsibility for the exodus. Diplomats want to keep the refugees in the South-East Asian region, to allow their speedy repatriation when the situation in East Timor stabilises, and the Philippines is being discussed as a possible destination.
"Last week there was a lot of momentum," a Western diplomat in Jakarta said yesterday. "But now I sense that the whole thing is losing steam."
Outside East Timor the highest number of refugees is in West Timor, where 200,000 are living in conditions of squalor and fear. But across the Indonesian archipelago there are smaller East Timorese communities, which have become the victims of a systematic campaign of intimidation.
In Lampung, Sumatra, East Timorese students have been told that they will now be treated as foreign students and have been evicted from their accommodation.
In Ujung Pandang, on the island of Sulawesi, 3,600 refugees are living in schools, mosques and churches under the control of the feared Aitarak militia, and students in Yogyakarta, central Java, have fled to Jakarta.
Unconfirmed reports from the capital speak of a training camp for 2,000 East Timorese, many of them press-ganged, who are being trained to return for incursions into East Timor.Reuse content