Refugees on Manus Island and Nauru might have to wait well into the new year before being resettled in the United States.
The federal government at the weekend announced it had brokered a one-off deal with the US, although exact details remain unclear.
Among the doubts is whether the arrangement will survive the installation of the Trump administration on January 20.
The Department of Immigration and Border Protection on Tuesday confirmed the transfer could take months - or perhaps longer for some people.
Secretary Michael Pezzullo said the process cannot be rushed, with necessary checks required under US law.
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"You are dealing with people all around the world and not everyone will be resettled by 20 January 2017," he told a Senate inquiry.
"I think we can state that to this committee with absolute certainty."
Mr Pezzullo also confirmed that a woman receiving treatment in Australia after being raped while in detention would need to return to Nauru if she wanted to be resettled in the US.
And if she was not accepted by the US, she would remain on Nauru "until other settlement options could be achieved".
One Nation leader Pauline Hanson has expressed some concern with the US deal and its potential lure factor.
"These people are going to a first-world country where they're going to have a wonderful life," she told ABC radio on Tuesday.
"As a one-off, yes it does solve the government's problem - as long as we don't have another flood that actually comes out to Australia."
Senator Hanson reiterated her support for the government's proposed lifetime visa ban for any asylum seeker who has arrived by boat, despite NSW One Nation senator Brian Burston saying the measure cannot be taken seriously as a deterrent compared to the lure of American citizenship.
