Officials in neighbouring West Timor say they were ordered to set up camps to handle tens of thousands of people - before the independence referendum took place. Since Saturday, more than 24,000 people have left East Timor and registered with the West Timorese government. Many more, who believe they are on militia hit-lists, have left or are in hiding.
The refugee co-ordination centre in Kupang said it had been told to prepare for a massive influx on 26 August, four days before the ballot. An official said the government was not so much running a refugee crisis as handling a transmigration programme. The official said thousands who had left would never go back to East Timor and were being found homes and jobs elsewhere.
In further evidence that the exodus is being run by the Indonesian government, officials said specific areas were being selected for evacuation and people were being advised to "pack up and get out".
The latest arrivals are mostly from the west of the territory. With them come the militia, who were given control of the camps and are making a show of force; armed militiamen are common in Kupang. Foreigners have no access to the camps and hundreds of refugees who back independence are trying to escape to Bali.
Humphrey Hawksley is a BBC world affairs correspondent