Government agencies have reportedly warned of national security implications of there are changes to the way medical transfers are processed for asylum seekers in offshore detention.

A briefing note from the Department of Home Affairs obtained by The Australian says the medical transfer bill will strip the government of its power to conduct proper security threat assessments or stop mainland transfers.

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

The changes, inspired by a push from Wentworth independent MP Kerryn Phelps, would mean any two doctors could request a medical transfer for those in offshore detention.

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

The security briefing – put together by ASIO and Australian Border Force – 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 new system could also see child molesters, rapists and murderers enter Australia, the government fears.

But Labor has stressed the doctors’ opinion could still be overruled by a minister on national security grounds, publishing legal advice it received in December to back up the claim.

Immigration Minister David Coleman says that power would not remove the potential for serious criminals to be transferred to Australia on medical grounds.

“Labor’s definition of security does not cover people convicted of serious crimes, including murder and offences against children,” he told AAP on Wednesday.

“The government’s advice on this issue is extremely clear.”

Labor leader Bill Shorten earlier responded to similar comments from Prime Minister Scott Morrison by saying he should be “ashamed of himself”.

“The fact of the matter is people who have done those crimes don’t get the refugee status unless the government’s missed them when they’ve assessed them as refugees,” he told reporters.

“The idea that somehow because you’re a Liberal you dislike those crimes more than if you’re someone else, I just get sick of that moral superiority and finger pointing.”