US Vice-President Mike Pence has reaffirmed that the Trump administration will honour the controversial refugee deal struck with Barack Obama, despite not liking it.

Made in the last days of the Obama administration, the United States agreed to resettle refugees from Manus Island and Nauru, as Australia seeks to close its off-shore detention facilities.

In a phone call to Prime Minister Malcolm Turnbull shortly after his election, President Donald Trump referred to it as the "worst deal ever" in a conversation later described as "tense".

Speaking to media following his bilateral meeting with Mr Turnbull in Sydney on Saturday, Mr Pence said the deal would go ahead, despite doubts over what Mr Trump had publicly labelled a "dumb" agreement.