Australian Prime Minister Malcolm Turnbull has said he is confident a refugee resettlement deal with the United States will go ahead, despite White House comments which seemed to cast doubt about its future under a Trump administration.

White House deputy spokesman Eric Schultz told reporters the deal to resettle in the US refugees currently held at Australian-funded offshore detention centres was reached with President Barack Obama, and it was the prerogative of each president to set policies.

 Australia and the US reach refugee deal

"We have one president at a time," Schultz said on Friday. "The president-elect, Donald Trump, will set the policies once he takes the oath of office."

Turnbull downplayed the comments when questioned by reporters in Sydney on Sunday.

"It's a very good arrangement and we are confident that we'll continue through the change of administration," the Australian Associated Press quoted him saying.

Australia announced last month that the Obama administration had agreed to take a substantial number of the 1,200 refugees held on Nauru and Manus Island in Papua New Guinea.

'Hasty' deal

The resettlement deal with the US came after Turnbull agreed in September to take part in a US-led programme to resettle refugees from Guatemala, Honduras and El Salvador as part of Australia's annual intake of 18,750 asylum seekers.

 UN blasts Australia over treatment of asylum seekers 

Whether Trump, who has advocated a ban on people from nations that had been "compromised by terrorism", honours the agreement is uncertain.

US homeland security officials were scheduled to begin assessing asylum seekers on Nauru this week.

Many asylum seekers at the camps are Muslims who have fled conflicts in Iraq, Syria, Afghanistan and Pakistan.

Ian Rintoul, from the Refugee Action Coalition, said it was very clear the deal Australia struck with the US was not airtight.

"The announcement was very hastily put together because they weren't expecting Trump to win and then it came very clear the whole deal could roll over," he said.

Source: Agencies