The White House and the US State Department are at odds over the fate of a deal to resettle refugees from Australia's offshore detention centres.

Key points: White House says Trump is still evaluating the deal

White House says Trump is still evaluating the deal State Department says refugees will come to US but in accordance with Trump's recent executive order

State Department says refugees will come to US but in accordance with Trump's recent executive order Peter Dutton backs deal's future, criticises 'hate media'

The White House today said President Donald Trump has been considering whether to honour the deal to take refugees from Manus Island and Nauru, negotiated by the Turnbull Government in the latter days of the Obama administration.

However, the State Department told the ABC the deal would go ahead.

An official from the State Department confirmed the deal would continue, but said refugees would only come to the US in accordance with Mr Trump's recently signed executive order.

Sources said the President had very reluctantly agreed to the arrangement due only to the close relationship with Australia, but is not otherwise in favour of the deal and would prefer it did not proceed.

The order — signed last month — banned travel from seven majority Muslim countries for 90 days, suspended all refugee admissions for 120 days and suspended the entry of Syrian refugees indefinitely.

The comments from the State Department came after the White House issued a statement to the ABC saying that "the President is still considering whether or not he will move forward with this deal at this time".

"He is considering doing it because of the long and good relationship we have with Australia."

The statement mirrored comments made in a phone call to the ABC from a senior White House official yesterday.

Michael Anton, a spokesman for the White House National Security Council, also confirmed to the ABC and others that the President had been evaluating the agreement.

The White House statement is also at odds with the Australian Government's message, with Immigration Minister Peter Dutton publicly backing the deal's future in the same hour the White House threw doubt on it.

Talking to Sydney radio station 2GB, Mr Dutton described the Government as being in a "good position" regarding the deal and took aim at the "hate media" — including the ABC — over its coverage.

"The Prime Minister has spoken to President Trump and we had agreement from President Trump that he would continue the arrangement," he said.

"It seems to me that some of the hate media journalists on the left wing debate in this country are adamant that they want to use these people as pawns."

On Wednesday, press secretary Sean Spicer told reporters in Washington the deal would go ahead, subject to the "extreme vetting" of approximately 1,250 refugees.

Those comments were subsequently walked back, but Australian officials said the Trump administration had already told officials to ramp up arrangements needed to get the process underway.

Prime Minister Malcolm Turnbull said Mr Trump gave him a personal assurance during a phone call on the weekend that the deal will be honoured.

When pressed again on the issue today, Mr Turnbull told reporters he had received assurances from Mr Trump over the deal.

"That assurance was confirmed by the President's spokesman in the briefing room of the White House," he said.

"Our officials, our respective officials, are continuing to work on the implementation of the arrangements. That's the position."

In a statement, the US embassy in Canberra said Mr Trump's decision to honour the refugee agreement had not changed and Mr Spicer's comments stand.

"This was just reconfirmed to the State Department from the WH and on to this embassy at 1315 Canberra time," it read.