Louise Williams, Jakarta – Tens of thousands of Muslim migrant workers will be repatriated from West Kalimantan following months of ethnic clashes, in a blow to Indonesia's ambitious program of moving millions of people away from the overpopulated centre and onto its remote outlying islands.

Since last December the indigenous Dayaks of West Kalimantan have been fighting a bloody war with migrant settlers from the island of Madura, just off the coast of Java, which supports 120 million of Indonesia's 200 million people. Hundreds of people are believed to have died in the violence and local authorities say at least 2,500 homes were destroyed. The Minister for Transmigration, Mr Siwono Yoduhusodo, said at least 20,000 Madurans remained in refugee camps and were too traumatised by the violence to return to their homes. He said they would be resettled in another area under a government-funded program.

The Governor of West Kalimantan, Mr Aspar Aswin, said some regions would not welcome back the Madurans following their role in the conflict.

The Madurans were blamed for sparking the ethnic war following the rape of a Dayak woman in late December. Similar allegations of atrocities committed against Dayak tribespeople, including the murder of pregnant women, provoked a bloody "payback" in which the Dayaks returned to the ritual of head hunting for the first time in almost 100 years. The Dayaks believe that transmigration and mining and plantation development have robbed them of their spiritual lands, destroyed their practice of shifting cultivation and left them as second-class citizens on the edges of the towns. Mr Siwono said the conflict had destroyed only seven out of 264 transmigrations sites in West Kalimantan and maintained that in some areas Dayaks and Madurans continued to live harmoniously.