The United Nations refugee agency has accused the Turnbull government of failing to honour a "clear understanding" that it would allow some people on Nauru and Manus Island to resettle in Australia. 

In a statement strikingly at odds with the Turnbull government's public position that no refugees now in offshore detention would step foot in Australia, the UN High Commissioner for Refugees said the agency had agreed to help administer the deal between Australia and the United States on the understanding there would be exceptions for vulnerable people with family ties in Australia.

"Last November, UNHCR exceptionally agreed to help with the relocation of refugees to the United States following a bilateral agreement between Australia and the US," commissioner Filippo Grandi said in a statement released Monday afternoon.

"We agreed to do so on the clear understanding that vulnerable refugees with close family ties in Australia would ultimately be allowed to settle there."

He said that the UNHCR had "recently been informed by Australia that it refuses to accept even those refugees".

"This means, for example, that some with serious medical conditions or who have undergone traumatic experiences, including sexual violence, cannot receive the support of their close family members residing in Australia."

The Turnbull government has always publicly vowed that no refugees on Nauru or Papua New Guinea will be resettled in Australia. Immigration Minister Peter Dutton told Sky News on Sunday that "people will not be coming to Australia" and there was no contingency in which the government might change its mind and make exceptions.

And a spokeswoman for Mr Dutton said on Monday: "The position of the Coalition government has been clear and consistent: those transferred to [regional processing centres] will never settle in Australia."

But a spokeswoman for the UNHCR's regional representation in Canberra subsequently told Fairfax Media: "An understanding was clearly reached over a number of months, and over a number of meetings, including with Minister Dutton himself."

Under the deal struck between Mr Turnbull and former US president Barack Obama, the US would take people from Australia's offshore detention system who were found by the UN agency to be refugees and who did not pose security risks.

The UN body, which helps arrange the resettlement of refugees, now had "no other choice but to endorse the relocation of all refugees on Papua New Guinea and Nauru to the United States, even those with close family members in Australia", Mr Grandi said.

The US is expected to accept hundreds of refugees but it is likely that some will not be accepted and it remains unclear what will happen to them. The US is also applying what the administration of US President Donald Trump has called "extreme vetting" for possible security risks.

Mr Grandi said that staying on Manus Island or Nauru, or transferring to Cambodia, with which Australia also has a deal, were "wholly inappropriate" for people who had already gone through suffering.

"There is no doubt these vulnerable people, already subject to four years of punishing conditions, should be reunited with their families in Australia. This is the humane and reasonable thing to do."

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