Paul Dillon, Ambon – The detention of five members of Indonesia's notorious Kopassus (Special Forces) in the Maluku islands has raised fears the Australian-trained commandos are engaging in an East Timor-style dirty tricks campaign.

A senior military source has confirmed five unarmed Kopassus commandos were arrested after being spotted aboard a ship that arrived in the Malukan capital of Ambon on Sunday. The source said two Indonesian navy officers boarded the ship, Lambelu, outside the port to check for suspicious people and prevent the secret off-loading of weapons and munitions to Muslim forces engaged in the 19-month conflict.

The officers spotted the five long-haired Kopassus members and passed the information to their commander. Kopassus commandos, who are feared by the population of the sprawling island archipelago, from separatist Aceh province to Papua, usually wear their hair long. The navy was ordered to detain the commandos if they could not produce travel orders, but their fate is unclear.

Records show the Kopassus men boarded the vessel on Buru Island, a stronghold and staging point for Laskar Jihad (Legion of the Holy War), an extremist Muslim group from Java whose arrival here in May resulted in a sharp escalation in the number and scale of clashes between Christians and Muslims.

Ninety per cent of Indonesia's 210 million people are Muslim, but in Maluku province (formerly the Spice Islands) roughly half the population is Christian. The source said the presence of Kopassus members was unusual. He did not know the current whereabouts of the five, but said they did not disembark in Ambon.

The Indonesian Special Forces were responsible for organising some of the most notorious East Timorese militias, who laid waste to the former Portuguese colony following the independence vote last August. More than a thousand people died and East Timor's infrastructure was destroyed in a three-week orgy of militia violence before the arrival of an Australian-led multinational force in late September.

Meanwhile, authorities and civic leaders in Jayapura, capital of the Indonesian province of Irian Jaya, have agreed to let about 1200 refugees from the Maluku islands come ashore from an impounded state ferry. Prompted by past demonstrations against dumping refugees in the region, the authorities had barred the ship from berthing at the port and its passengers from disembarking.