Prime Minister Scott Morrison has dismissed claims the Coalition made a secret deal with crossbench senator Jacqui Lambie to secure her vote to dismantle the Medevac scheme.
Senator Lambie helped the repeal bill pass 37 to 35 on Wednesday, putting an end to the medical evacuation scheme which has helped get sick asylum seekers off Manus Island and Nauru.
The Tasmanian crossbencher said she had put a proposal to the Morrison government during the negotiations, but refused to say what, citing national security concerns.
She said her proposal would lead to an outcome where "our borders are secure, the boats have stopped and sick people aren't dying waiting for treatment".
"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," Senator Lambie said through tears.
"I can't let the boats start back up and I can't let refugees die, whether it's sinking into the ocean or waiting for a doctor and I am voting to make sure that neither of these things happen."
But the Coalition's leader in the Senate, Mathias Cormann, denied a deal had been done to secure her vote.
While Senator Lambie had put a plan to the government, they only gave her classified briefings on the situation in return, Senator Cormann said.
"There is no secret deal. There will be no change to our strong border protection arrangements. There will be no change to our strong national security arrangements. And there will be no change in the way we deal with the legacy caseload that Labor left behind when you were last in government," Senator Cormann said.
Mr Morrison chose his words carefully when asked about the deal.
"The only undertaking we've given is to implement our policies, that is it," Mr Morrison said.
"The government's policy is to ensure that we seek to resettle people who are on Nauru."
But Greens leader Richard Di Natale said that explanation did not add up.
"According to Senator Lambie that there was a proposal that was put to the government negotiated in secret, and yet the government denies it," Senator Di Natale said.
"Either Senator Lambie is lying or the government is lying."
Senator Lambie said she decided to vote with the government, as the medical evacuation scheme could not be left the way it was.
"Medevac is not a national security threat, but there are real problems with the way it's operating," Senator Lambie said.
"There are problems that sit at the centre of its operation. They cannot be amended away. The Labor Party and the Greens might think everything is A-OK, but I'm not comfortable with it."
While proponents of Medevac said doctors, not bureaucrats, should decide whether asylum seekers were sick enough to come to Australia, Senator Lambie said "doctors aren't elected".
"To those who say that doctors should make the final call on matters like this, doctors don't make our health policy. The final decision-maker for health policy is the Minister for Health. You can take advice from doctors, but doctors aren't elected. They aren't accountable to the public. They can't be voted in or out," Senator Lambie said.
"We have a system here where we let experts give advice, but we do not let them make the final decision on matters of this nature. Medevac lets the doctors make the call and the minister has an incredibly limited ability to overrule it.
"If you care about the government being accountable to the people, that should bother you. It bothers me. But it doesn't bother me enough to let people die so I'm faced with a question of what to do. Do I repeal the legislation or let it sit there? Not as perfect as the activists would have you believe. But not as terrible as the media loudmouths would have you believe either."
I can't let the boats start back up and I can't let refugees die, whether it's sinking into the ocean or waiting for a doctor and I am voting to make sure that neither of these things happenSenator Jacqui Lambie
More than 170 refugees and asylum seekers have been brought to Australia under the Medevac scheme, after it passed the parliament in February.
Home Affairs Minister Peter Dutton said the scheme had served as a "back door" into Australia.
"Today we close that back door," Mr Dutton said,
It means the 471 refugees and asylum seekers left in offshore detention will have to fight for future medical transfers through the courts.
Refugee advocates have already sprung into action to support asylum seekers in Papua New Guinea and Nauru.
Canberra nun Sister Jane Keogh said the repeal had galvanised her to keep fighting on behalf of the men of Manus.
"I'm not falling in a heap. It's energised me. I'm gearing up to see where to fight next," Sister Keogh said.
International medical humanitarian organisation Médecins Sans Frontières renewed its call for all asylum seekers to be evacuated from offshore detention and resettled.
"Preventing access to medical care as a policy tool is unethical and harmful to vulnerable people and the entire medical profession," a spokesperson said.
"The repeal of Medevac flies in the face of patient's best interests. A lifeline has been ripped from the hands of people whose only crime may have been seeking safety from persecution."
The repeal came after Senator Cormann moved quickly to suspend standing orders on Wednesday morning, fuelling speculation a deal had been struck with the influential Tasmanian crossbencher.
Labor senator Katy Gallagher moved a motion to try to force the government to table documents related to any deal before the bill could pass. It was unsuccessful.
Labor senator Penny Wong accused Coalition ministers of running to the Senate "like lemmings" to vote on a deal they had not seen.
"We should not be voting on legislation which is predicated on a backroom deal no one has seen," Senator Wong said.
Senator Di Natale said the Greens would now work with other parties in the Senate to try and force Senator Lambie to reveal her hand.
"This is giving a middle finger to the Australian parliament, to act without any transparency or accountability," Senator Di Natale said.