By Harry Pearl

SYDNEY (Reuters) - Australian Prime Minister Malcolm Turnbull said on Sunday he was confident a refugee resettlement deal with the United States would 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 U.S refugees currently held at Australian-funded offshore processing centers was reached with President Barack Obama, and it was the prerogative of each president to set policies.

"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 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.

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

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

U.S. Homeland Security officials were scheduled to begin assessing asylum seekers on Nauru this week.

Many of 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 U.S. 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.

(This version of the story has been refiled to correct typographical errors in first and third paragraphs)

(Reporting by Harry Pearl; Editing by Eric Meijer)