US officials interviewing refugees at the Nauru detention centre left the facility abruptly at the weekend, casting fresh doubt over whether the plan to resettle detainees in America would proceed.

The Reuters news agency said the officials had halted their screening interviews two weeks early - and just a day after the United States reached its annual refugee intake cap of 50,000.

But Foreign Minister Julie Bishop says the US security screening process is "progressing as we expected".

"The United States is upholding the agreement. We have been given assurances by President Trump and Vice-President Pence and others, that the agreement will be adhered to," she told the ABC's Insiders program.

"The United States, like Australia, has a quota each year for the refugee intake. I understand that the quota has been fulfilled for this year. It kicks over again on October 1. But I have no doubt that the agreement is progressing."

The Turnbull government struck the refugee deal with the Obama administration last year but its future has been uncertain since Donald Trump took over. The US president described it as a "dumb deal" and clashed with Prime Minister Malcolm Turnbull over it during a notorious phone call earlier this year.

The US Department of Homeland Security also said the program was continuing and officials were planning return trips.

"It is not uncommon for the dates of tentatively-planned refugee circuit ride trips worldwide to change due to a wide variety of factors," it said.

But Behrouz Boochani, a refugee and journalist currently held on Manus Island, said the news was frustrating for him and the 1780 other refugees on Nauru and Manus.

"The US deal has already been clouded with uncertainty and we worry that it is just part of a cruel game. When the deal was first announced, it brought people some hope. But day by day that hope has diminished, and now this news brings more disappointment and doubt."

Progressive activist group GetUp said the deal was in "crisis". The group's Matthew Phillips, said the camps should be evacuated and the detainees brought to Australia.

"Turnbull's US deal was announced eight months ago, yet not one refugee has been taken to safety in the US," he said.

In exchange for America's help taking the people from the Pacific islands - some of whom have been languishing there for up to four years - Australia will take Central American refugees from a centre in Costa Rica, where the US has taken in a large number of people in recent years.

Australia hopes to close the Manus Island centre in the coming months.

With wires