Home Affairs Minister Peter Dutton says a move from the Greens, Labor and independents to allow more medical transfers of asylum seekers will threaten national security.

Mr Dutton says Labor leader Bill Shorten has ignored classified security advice from ASIO and Border Force.

"The advice is clear in relation to the outcomes of Mr Shorten's actions and he needs to rethink his position. And he needs to overturn his support of this bill," Mr Dutton said.

But Labor says its own legal advice shows the minister would still have the ability to reject medical transfers on national security grounds.

Labor supports the proposed amendment, which has already passed the Senate and is expected to be voted on in the lower house as early as next week.

The coalition faces a potentially deadly loss on the vote and is doing everything it can to avoid it.

Mr Dutton says the proposal will "dismantle" offshore detention and hand the final say to the two doctors requesting medical transfers.

"Doctors including Dr Bob Brown and Dr Richard Di Natale, potentially, can provide the advice," he told reporters in Brisbane on Thursday.

But, under the proposed laws, the eligible doctors will be specially nominated by a peak medical body and approved by the minister, so it's unlikely former Greens leader Dr Brown or his successor Senator Di Natale will be involved.

"Neither Bob nor I are currently registered so we couldn't sign off a transfer. To think this bloke was making daily decisions about the fate of innocent people," Senator Di Natale told AAP.

The Senate recently amended a government bill to allow two doctors to request a medical transfer for those in offshore detention.

A minister would then be required to review their case within 24 hours and, if they reject it, an independent health advice panel would review it.

Labor accused the coalition of politicising government agencies after the classified security advice from ASIO and Border Force was given to a newspaper on Thursday.

"It's classified for a reason. It's not meant to be read about in the newspaper," shadow treasurer Chris Bowen told reporters.

A note from the Department of Home Affairs published in The Australian also warns that 1000 asylum seekers from Manus Island and Nauru could be given the tick of approval to come to Australia within weeks.

The coalition says the proposed new transfer system could also see child molesters, rapists and murderers enter Australia.

While Labor's advice states doctors' opinions could still be overruled by a minister, the government says "national security grounds" only covers a narrow definition and does not include criminal acts.

Australian Associated Press