Prime Minister Malcolm Turnbull has attempted to quash concerns Donald Trump is having second thoughts about the refugee deal struck between Australia and the United States.

Confusion hangs over the deal amid reports Mr Trump is yet to fully endorse the agreement, despite assurances from his press spokesman, Sean Spicer.

On Wednesday morning (AEDT), Mr Spicer said the swap would go ahead, saying refugees heading to the US from Manus Island and Nauru would undergo “extreme vetting”.

But hours later, the ABC reported the White House had contacted it to say that Mr Trump was still considering the deal and that it was not known where the number of refugees Mr Spicer said the US would take – 1250 – had come from.

We were told in WH briefing today that Aus-US refugee deal is going ahead,now White House has told me @POTUS hasn't made a final decision

— Zoe Daniel MP (she/her) (@zdaniel) January 31, 2017

But after that revelation, Mr Turnbull said he will hold the president to the pair’s earlier commitment to the deal.

In response to The New Daily’s questions regarding the latest on the refugee swap following the reported White House backflip, a spokesperson for Mr Turnbull said the PM “has received assurances [the deal would go ahead] directly from President Trump”.

Mr Turnbull doubled down on that response when answering questions at the National Press Club on Wednesday afternoon.

“The Trump administration has committed to progress with the arrangements to honour the deal, if you like, that was entered into with the Obama administration, and that was the assurance the president gave me when we spoke on the weekend,” Mr Turnbull said.” the prime minister told reporters in Canberra on Wednesday.

“That was the assurance the president gave me when we spoke on the weekend.”

Mr Turnbull also confirmed the US would be heavily vetting the refugees.

“They [the US] will do their own extremely rigorous vetting of people that are the subject, or potentially the subject, of the agreement,” he said.

The New Daily has contacted the Department of Immigration and Border Protection, and that department’s minister, Peter Dutton, for clarification on the state of the deal.

Mr Turnbull came under heavy criticism earlier this week when he refused to denounce Mr Trump’s travel ban.

Some believed Mr Turnbull’s silence was an attempt to avoid jeopardising the refugee deal the president is reportedly still considering. 

On Saturday, the president put a four-month hold on allowing refugees into the US and temporarily barred travellers with passports from seven Muslim-dominated countries.

Asylum seekers remain in detention across Nauru and Manus Island. Photo: AAP

Labor Senate leader Penny Wong said the PM would have questions to answer over the White House’s reported backflip.

“Does the prime minister actually know what the agreement is and whether it will be implemented? It appears there are very mixed messages,” she said.

Senator Wong said Labor supported the deal but it was another case where a government announcement had quickly unravelled.

“Look, we want the agreement to work,” she said. “We have been saying for some time that the government does need to find resettlement options for the people on Manus.”

Ms Wong also dismissed the suggestion the prime minister was right to avoid criticising Mr Trump’s travel ban to safeguard refugee deal negotiations.

“Are you seriously suggesting that the US Government would say to Australia, ‘We’ll only do this deal if you don’t criticise us?’ I can’t imagine that’s the basis of our relationship with the United States,” she said.

White House says yes, then no

Earlier on Wednesday Mr Spicer told a White House press briefing the deal, struck between the Obama administration and Turnbull Government, would go ahead and include about 1250 refugees.

Many are from countries covered by the new administration’s bans on entry to residents from seven majority-Muslim nations.

White House Press Secretary Sean Spicer was contradicted later in the morning. Photo: Getty

“There will be extreme vetting applied to all of them,” he said. “That is part and parcel of the deal that was made, and it was made by the Obama administration with the full backing of the United States Government.”

According to the latest statistics from the Immigration Department, there are 871 people on Manus Island and 383 people on Nauru.

The ABC reported most of the refugees are from Iran, with some also from Iraq and Somalia, three of the countries on the Trump administration’s travel-ban list.

Mr Turnbull spoke with Mr Trump by phone on Sunday, during which time it is understood the president agreed to honour the deal.

Before the call, Mr Turnbull said there was a section in Mr Trump’s executive order which stated officials could still admit refugees under pre-existing international agreements.

– with ABC and AAP