Prime Minister Scott Morrison has denied striking a deal with crossbench Senator Jacqui Lambie over the repealing of laws designed to give doctors more say in medical transfers of refugees in offshore processing.

The medevac repeal bill passed 37 votes to 35 on Wednesday delivering on a Coalition promise, after the laws were passed against its wishes in February.

Mr Morrison said scrapping the transfer provisions would restore integrity to border security after Senator Lambie's crucial support sealed its fate.

"The only undertaking we've given is to implement our policies, that is it," he said.

"We’ve always understood that that type of loophole doesn’t strengthen our borders - it weakens them."

AAP

A tearful Senator Lambie backed the federal government's repeal after previously citing one condition was needed to secure her support.

Prior to the vote, Senator Lambie became emotional as she explained the reason for her decision.

“I’m not being coy or silly when I say I genuinely can’t say what I proposed,” she told the Senate.

“I know that’s frustrating to people and I get that – I don’t like holding things back like this but when I say I can’t discuss this publicly because of national security I am being 100 per cent honest to you.”

It has been speculated the government could have agreed to send refugees from offshore processing to New Zealand after a similar arrangement with the US has ended.

But Mr Morrison remains coy over any deal, and has criticised medevac for allowing people to "get around the laws" and find their way to Australia.

"She has the assurance that the government will implement its policies," he said.

"We have always taken the actions necessary to ensure Australians can have confidence in the way our borders are managed."

In relation to the prospect of a New Zealand deal, he said: "the government is always looking at ways to resettle those who ore on Nauru."

"We will continue to use the arrangements that we have in place to be able to resettle people and that is the assurance that we have provided," he said.

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Senator Lambie said she was satisfied that conditions are now in place to allow medevac to be repealed and ensure refugees won't die "sinking in the ocean or waiting for a doctor".

“My hand is on my heart and I can stand here and say that I would be putting at risk Australia’s national security and national interest if I said anything else about this,” she said.

“We’ve worked to an outcome I believe we both want, which is an outcome that our borders are secure, the boats have stopped and sick people aren’t dying for treatment.”

STATEMENT ON MEDEVAC



In light of considerable community interest in my position on the Government’s legislation to repeal the Medevac provision, including the thousands of Australians who have petitioned me directly, I wish to outline my final position on the bill.#auspol pic.twitter.com/Ink1iBU4cn — Jacqui Lambie (@JacquiLambie) November 27, 2019

Thirteen medical colleges and more than 5,000 doctors had warned against any attempt to wind back the medevac laws.

But Home Affairs Minister Peter Dutton said "people were already receiving" appropriate medical treatment before the medevac regime.

He described the legislation as a law designed to provide a "backdoor" to Australia, which was now closed.

"Labor took a decision to weaken our border protection policies and we've taken a decision today to strengthen our border protection policies," he said.

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But Labor home affairs spokeswoman Kristina Keneally has questioned a lack of transparency around the alleged deal clinched between the Government and Senator Lambie.

"The parliament and the Australian people have a right to know what this secret deal is," she said.

"A deal between the Morrison government and Senator Lambie to drive a stake through the heart of medevac and they're keeping it secret from this parliament and from the Australian public.

"The public has a right to know if the Government and the Prime Minister have done a backflip and decided to accept the New Zealand offer – they should announce that."

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Greens leader Richard Di Natale also accused the Morrison government of misleading the Parliament for saying no “secret deal” had been reached with Senator Lambie.

“We had Minister Cormann say that there was no deal – now we’ve had Senator Lambie say there is a deal - who is lying?”

“Someone is misleading the Senate about one of the most important pieces of legislation that has been before this Parliament.”

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Since the laws were passed, more than 180 people have been transferred to Australia from Nauru and Papua New Guinea.

There are more than 200 refugees and asylum seekers left on PNG and more than 250 remaining on Nauru.

Under medevac, two treating doctors could recommend a medical transfer to the Department of Home Affairs.

The request was then considered by the Minister for Home Affairs, who could deny it on national security grounds, or if they had concerns on serious character grounds.

The minister could also deny on health grounds – in this event, it went to the Independent Health Advice Panel for review.

With additional reporting from wires.