"Between 9 and 10 am (2300-0000 GMT) this morning, they had all been moved," PNG police spokesman Chief Superintendent Dominic Kakas told AFP, adding that the men were moved to two of the three transition facilities.
"It's empty. The military have taken back their base," he added of the Manus camp, which is located on a PNG naval base.
Video and photos posted by the refugees on social media showed uniformed police swinging and poking long metal poles at detainees and dragging them from their rooms towards buses bound for the transition centres elsewhere on Manus.
Police, engaged in an operation they dubbed "Helpim Friends", had vowed not to use force against the refugees, who have been refusing to leave the camp since Australia declared it closed on October 31.
Food, electricity and water supplies were shut off in a bid to get the detainees to move to the new facilities.
Australia's Immigration Minister Peter Dutton welcomed the news, and accused refugee advocates of making "inaccurate and exaggerated claims of violence and injuries" during the move Friday.
He also insisted that the alternative sites were habitable, despite detainees and human rights groups, including the UNHCR, saying the new camps were not ready to take in the refugees.
They had also raised concerns about the men's safety among a local population that has shown them hostility.
"These men are scared, they are exhausted and they are despairing," Amy Frew, a lawyer at the Australia-based Human Rights Law Centre, said earlier Friday.
"After four and a half years of limbo and uncertainty they still have nowhere safe to go," she said.
"This morning's actions show that whatever they do, wherever they go, their safety cannot be guaranteed until they are evacuated from Papua New Guinea."
Offshore policy questioned
The Manus camp initially housed around 600 refugees, most of whom have been there since 2013, but around 200 moved voluntarily to the new centres earlier this month.
Iranian journalist and refugee Behrouz Boochani, who has acted as an unofficial spokesman for the men and was taken by police to one of the new centres on Thursday, said four full buses of refugees were taken from the closed camp Friday morning.
"The refugees are going to leave the prison camp. So many are in the buses and are on the way to the new camps," he said.
The UNHCR said it was disturbed by the use of force by PNG police.
"UNHCR reminds Australia of its obligation to take full responsibility and provide effective protection, safety and lasting solutions for all refugees and asylum-seekers in cooperation with the Papua New Guinean authorities," the organisation said in a statement Thursday.
The standoff with PNG authorities has drawn attention to Australia's harsh policy of sending asylum-seekers who try to reach Australia by boat to remote Pacific camps on Manus and Nauru.
The refugees are barred from resettling in Australia, but Canberra has struggled to transfer them to third countries, including the United States.
More about: #refugees