Their transfer to the Bomana Immigration Centre follows recent calls by PNG Prime Minister James Marape for the "full closure" of asylum seeker facilities on Manus Island.

Authorities shifted the men from the Hillside Haus facility on Manus Island early last month, initially telling them it was a temporary shift to hotel accommodation in the capital because repairs were being conducted on the centre.

On Sunday night, the men were moved to the new Bomana facility, which received $20 million in funding from the Australian government.

According to a notice obtained by refugee advocates, the men were told they would need to "surrender your mobile phone", any medication and pack belongings to prepare for the move to the new facility.

"You will not leave room. Your meals and drinks will be provided to you in your room. If you are on medication, we will administer to you," the document says.

The transfer leaves about 150 refugees and asylum seekers on Manus Island and 80 in temporary hotel accommodation in Port Moresby. Last month, Mr Marape said he wanted a "mutually workable timetable and closure program" of asylum processing on the island.

In a statement, Australia's Department of Home Affairs said the management of asylum seekers in regional processing centres was a matter for PNG authorities.

The department said PNG law permitted detention and removal of non-citizens who do not have a right to remain in the country.

"As the Papua New Guinea government seeks to resolve the regional processing caseload, it has determined that these failed asylum seekers should be detained pending removal," the department said.

"Papua New Guinea will continue to manage refugees in the community pending their resettlement in a third country, settlement in Papua New Guinea or voluntary departure."

According to the Australian government, no people determined to be refugees by the PNG government had been detained. People with "known migration pathways" were also not detained.

"Failed asylum seekers are encouraged to depart Papua New Guinea voluntarily and will be provided with support by the government of Papua New Guinea to do so," the department said.

There are about 50 refugees awaiting transfer to the United States under the people swap arrangement struck between the Turnbull government and Obama administration.

Refugee Action Coalition spokesman Ian Rintoul said the men had been moved to Port Moresby under a "ruse".

"There was never any intention of returning them back to Manus Island," he said.

"Many of those being detained are deemed not to be refugees although they have never had a refugee determination in PNG."

Mr Rintoul said the Bomana facility was "every bit as bad" as the now closed Lombrum centre on Manus Island.

He said people who had had their applications rejected should be released and have their cases reviewed.