The Government has quashed speculation the refugee swap deal between Australia and the United States may not go ahead, after American immigration officials who were interviewing refugees on Nauru left two weeks ahead of schedule.

Key points: Officials were scheduled to be on Nauru until July 26 but they left on Friday

Officials were scheduled to be on Nauru until July 26 but they left on Friday US immigration agency says refugee program is continuing and officials will return to Nauru

US immigration agency says refugee program is continuing and officials will return to Nauru Julie Bishop says deal is not in doubt

Julie Bishop says deal is not in doubt But Labor still concerned, says Government needs back-up options for resettling refugees

Three detainees told Reuters that US citizenship and immigrations who were vetting refugees on the island had halted screening interviews and left Nauru.

Their departure came one day after the US Government announced it has already filled its new, reduced quota of 50,000 refugees for the fiscal year, which means no more refugees will be accepted until October unless they have a bona fide family connection in America.

The US Citizenship and Immigration Services (USCIS) released a statement saying the refugee program is continuing and that officials will return to Nauru.

"We do not discuss the exact dates of USCIS' circuit rides to adjudicate refugees' applications. However, we are planning return trips," the agency said in a statement.

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

Foreign Minister Julie Bishop said that showed the deal was not in doubt.

"I understand that the matter is progressing as we expected," she told Insiders.

"The United States is upholding the agreement. We have been given assurances by both President Trump and Vice-President Pence that the agreement will be adhered to.

"I have no doubt that this agreement is progressing as the relevant US authority confirmed this morning."

"US [officials] were scheduled to be on Nauru until July 26 but they left on Friday," one refugee told Reuters, requesting anonymity as he did not want to jeopardise his application for US resettlement.

Labor says Government has 'dropped the ball'

US citizenship and immigration officials vetting refugees on Nauru reportedly left the island abruptly. ( Supplied )

Labor's defence spokesman Richard Marles earlier said he was concerned the deal could fall over, and warned the Government needed to come up with back-up options to resettle the refugees.

"All their eggs now are in the US basket," he told ABC News.

"They need to be looking at a whole lot of other options to make sure that hope and a future can be found for those people who are in those facilities.

"It's a very important deal, it needs to go through and it's good that the Americans are saying it's going to be continue to be honoured.

"But this Government has really dropped the ball over the last few years about those facilities and they need to be more active."

The Immigration Department declined to comment on the whereabouts of the US officials or the future of a refugee swap agreement between Australia and the United States.

The resettlement deal with the US was announced by Prime Minister Malcolm Turnbull last year, with Australia agreeing to consider resettling Central American refugees from a centre in Costa Rica while the US promised to consider taking refugees from Manus Island and Nauru.

US President Donald Trump described it as a "dumb deal", and his administration said it would only honour it to maintain a strong relationship with Australia and then only on condition that refugees satisfied strict checks.

The swap is designed, in part, to help Australia close both Manus and Nauru, which are expensive to run and have been widely criticised by the United Nations and others over treatment of detainees.

The US Government confirmed on Thursday that its refugee intake cap of 50,000 people had been reached with the new intake year not due to begin until October 1.

Exemptions could be made for those who have a "credible claim to a bona fide relationship with a person or entity in the United States", following a decision from the US Supreme Court last month reviving elements of Mr Trump's travel ban while it considers the legality of the order.

Given the risky boat journey the refugees in Manus and Nauru undertook to try and reach Australia, it is unlikely many of them have strong family ties to the United States, experts said.

An indefinite postponement of the deal would have significant repercussions for Australia's pledge to close a second detention centre on Papua New Guinea's Manus Island on October 31.

Only 70 refugees, less than 10 per cent of the total detainees held in the camp, have completed US processing.

ABC/Reuters

