Seventy men, believed to be Iraqis and Iranians, have been flown off Manus Island, following allegations of sexual assaults at the centre.
It's expected the remaining detainees will also be removed from the facility on Papua New Guinea shortly.
Immigration Minister Tony Burke told ABC this morning he had "already signed off" on those currently on Manus being rotated to other centres in Australia's detention centre network prior to finding out about the abuse claims.
The 70 men, believed to be of Iraqi and Iranian origin, were flown out about 3.30pm (AEST) on Wednesday.
A PNG immigration official told journalists he believed the men were headed to Australia.
Speculation is also rife Australian Immigration Minister Tony Burke will visit Manus Island on Thursday.
The departure of the asylum seekers comes amid allegations of daily sexual assaults at the centre.
Amid torrential rain at Manus' Momote airport, some of the men waved at journalists as they boarded the plane on Wednesday.
The chief executive of Manus Island's only hospital says he has heard nothing about alleged rapes at an Australian-run asylum seeker centre.
Dr Otto Numan told journalists on Wednesday his staff treat asylum seekers twice a week.
"I've never been involved in the medical treatment of anyone from the regional processing centre in Lombrum for treatment of sexual assault," he said.
"Also I haven't been informed of any."
Police also said they had not heard any reports of rape at the centre, but have investigated other incidents, such as minor assaults.
The former head of occupational health and safety at the centre, Rod St George, alleged on Tuesday night acts of self-harm and attempted suicide were occurring "almost daily" on Manus Island.
"I've never seen human beings so destitute, so helpless and so hopeless before," he told SBS's Dateline program.
"In Australia, the facility couldn't even serve as a dog kennel. The owners would be jailed."
PNG immigration officials and police tried to stop journalists filming the two busloads of asylum seekers boarding the plane.
One police officer said he was doing so at the request of security firm G4S.
This is despite a PNG immigration official earlier telling journalists it was OK to film.