The 43 Papuans, who reportedly include prominent pro-independence activists and their families, arrived on the northern coast of mainland Australia on Wednesday aboard an outrigger canoe in an apparent bid for asylum.
The political nature of their flight from Indonesia was highlighted by a banner strung on their canoe that accused Indonesia of "genocide" in West Papua, a former Dutch colony that Indonesia took over in the 1960s.
The incident threatened to upset delicate Australian-Indonesia relations at a time when the two countries are negotiating a new security treaty that is expected to include a pledge by Canberra not to interfere in provinces like Papua.
After carrying out initial health checks on the Papuans in a town on northern Australia's remote Cape York Thursday, Australian authorities flew the group aboard an air force transport plane overnight to Christmas Island, an Australian territory in the Indian Ocean, the immigration department said.
"The men in the group will be accommodated at the Phosphate Hill Detention Centre, while the women and children will be placed in staff housing," department spokeswoman Sandi Longan said.
Move criticized
Human rights groups and the opposition Labor Party criticised the decision to move the asylum seekers to Christmas Island rather than process their asylum claim on the mainland.
"I don't understand when there's excess capacity at mainland detention centers, why there's a need to take these asylum seekers as far away as possible from the best legal teams," said Tony Burke, immigration spokesman for the Labor Party.
"By all accounts, we're yet to see any argument why these individuals would not be found to be genuine asylum seekers, I can't see why Christmas Island's appropriate in this case," he said.
Australian media reports said Indonesian officials were allowed to meet with the Papuans before they were moved to Christmas Island, but no details of the encounter were made public.
A spokesman for the Indonesian embassy in Canberra earlier said any claim for asylum by the group would be "baseless".
But a foreign ministry spokesman in Jakarta said that Indonesia was remaining open minded about the incident and wanted to "manage this case well".
Indonesia won sovereignty over Papua, which was then called West Irian, in 1969 after the UN allowed an integration referendum with a public show of hands by a few hundred hand-picked tribal leaders.
The vote was labelled a sham by critics.
Poorly organised separatists have since been fighting a sporadic and ill-armed guerrilla war, amid charges by international human rights groups of widespread abuses by Indonesian military forces.