Australian Prime Minister Malcolm Turnbull announced after his weekend phone call with Trump that the president had agreed to honour the deal.

This was despite the agreement originally being struck by former President Barack Obama and last week Trump placing a temporary ban on refugees being admitted to the US and other strict US border measures targeting seven countries including Iran, Iraq and Syria.

White House press secretary Sean Spicer told reporters on Tuesday that the deal – specifically related to 1250 people – would go ahead, but that the refugees would have to clear “extreme vetting”.

“Part of the deal is they have to be vetted in the same manner that we are doing now. There will be extreme vetting applied to all of them,” he said.

“The president, in accordance with that deal to honour what had been agreed upon by the US government, and ensuring that vetting will take place in the same manner that we are doing it now, it will go forward.”

The refugees are being held on Papua New Guinea’s Manus Island and Nauru.

Shortly after the press conference, the ABC reported a White House source saying Trump was still considering whether the agreement would go ahead.

The ABC’s US correspondent, Zoe Daniel, reported she had received a follow-up phone call from a source which cast doubt Spicer’s statements.

The White House source said if the President did decide to honour the deal, it would only be because of America’s “longstanding relationship with Australia”.

Meanwhile, the Trump administration is facing continued internal dissent over the travel ban imposed on refugees and immigrants from seven Muslim-majority countries.

About 900 US State Department officials are said to have signed an internal dissent memo protesting the ban.

A senior State Department official has confirmed the memorandum has been submitted to acting Secretary of State Tom Shannon through the department’s “dissent channel,” a process in which officials can express unhappiness over policy.

White House spokesman Sean Spicer said on Monday he was aware of the memo but warned career diplomats they should either “get with the program or they can go.”

A draft of the dissent memo seen by Reuters news agency argues that the executive order would sour relations with affected countries, inflame anti-American sentiment and hurt those who sought to visit the United States for humanitarian reasons.

It said the policy “runs counter to core American values of non-discrimination, fair play and extending a warm welcome to foreign visitors and immigrants.

Trump on Friday signed an executive order that temporarily bans refugees and people from seven Muslim-majority countries, sparking tumult at US airports and protests in major American cities.

The ban affects Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen.

Even before the executive order on immigration was issued, concern among State Department officials had been growing over news reports Trump was about to ease sanctions against Russia, one State Department official said, speaking on condition of anonymity.

The resignation of at least four top State Department officials, including Under Secretary for Management Patrick Kennedy, who formally left the department on Tuesday, also caused some unease among diplomats who worried about a power vacuum.

– InDaily with AAP and Reuters