The Turnbull government insists its refugee deal with the United States will happen, but it may be some months more before transfers begin, The Canberra Times reports.
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 Mr 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.
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."
Government says refugee deal still on despite doubts after US officials leave Nauru (The Canberra Times)