Australian authorities have flown 43 asylum seekers from the Indonesian province of Papua to a detention centre on Christmas Island in the Indian Ocean.
The group of 30 men, six women and seven children boarded a Royal Australian Air Force Hercules aircraft last night.
The Papuans were found on Cape York Peninsula on Wednesday after they reached Australia following a six-day voyage in an outrigger canoe.
A spokeswoman for the Australian immigration department, Sandi Longan said the refugees had been medically examined in Weipa and cleared for travel.
Ms Longan said the men in the group would be accommodated at the Phosphate Hill Detention Centre, while the women and children would be placed in what she described as "staff housing".
She said departmental officials would interview the group, and assess their claims for asylum, while on Christmas Island.
A spokesperson for the Indonesian foreign ministry, Yuri Thamrin, said they wanted to listen to the detainees.
Mr Thamrin said there was "a will to manage this case well".
Professor Donald Denoon, former professor at the Australian National University and expert in Pacific history, says the incident will strain the relationship between Australia and Indonesia.
"I think it puts a great deal of pressure on us, and draws very unwelcome attention to it. I think the anomaly of the situation is that the Indonesian government suspects Australia of fostering Papuan separatism, and nothing could be further from the mind of the Australian government. I mean certainly the West Papuans have a great deal of sympathy in the general population, but an official level, the Australian government is firmly opposed to their claims."