The Tasmanian crossbencher cast the deciding vote to repeal the Medevac laws on Wednesday, after weeks of intensive negotiations with the government.

More than 170 refugees and asylum seekers have been brought to Australia under the scheme, after it passed the parliament in February.

Its repeal means the 471 refugees and asylum seekers left in offshore detention will have to fight for future medical transfers through the courts or rely on ministerial discretion.

Asylum seekers had to wait two years on average for medical transfer under these provisions, an audit from the Asylum Seeker Resource Centre showed.

But lawyers and refugee advocates say there is a big question mark hanging over asylum seekers who were approved for transfer under Medevac but had not yet left Papua New Guinea and Nauru.

Canberra nun Sister Jane Keogh, who operates the Manus Lives Matter group, said she knew of at least 20 asylum seekers who'd been going through the Medevac process but had been unable to leave PNG as they had been placed in Bomana Immigration Centre.

Dozens of men who were deemed non-refugees were moved to the detention facility in August.

Home Affairs boss Mike Pezzullo acknowledged the Australian government needed to work through the situation "diplomatically" with the PNG government, when questioned in Senate estimates earlier this year. He also noted the Australian government was having similar troubles with the Nauru government blocking medical transfers.

Sister Keogh said she'd dealt with many asylum seekers who had been blocked two or three times from leaving PNG despite being approved under Medevac.

"A plane of asylum seekers had been due to come to Australia today," Sister Keogh said.

Refugee Legal's David Manne confirmed he knew of "quite a number" of asylum seekers who had been approved for transfer but blocked from leaving the country.

Mr Manne said the government needed to honour those transfers that were already approved.

"We call on the government to make good on the decisions made in line with the medical recommendations of doctors, where the minister approved applications on the basis of medical evidence," Mr Manne said.

Asylum Seeker Resource Centre's director of advocacy and campaigns Jana Favero also urged the government to transfer people who'd already been through the Medevac process.

"We do know there are people approved by the minister for transfer. We're asking for them immediately brought to Australia for treatment," Ms Favero.

However a spokeswoman for Home Affairs Minister Peter Dutton said those who had already applied under Medevac would be considered under the existing mechanism.

"Transfer for medical treatment remains available through standard medical transfer processes established in accordance with the transitory persons provisions in section 198B of the Migration Act," she said.

Senator Lambie had said her support was tied to a proposal she had put to the Coalition, but would not disclose publicly due to national security concerns.

It has been widely speculated that Senator Lambie had pushed for the government to reconsider an offer from the New Zealand government to resettle 150 refugees.

But Senate leader Mathias Cormann denied they'd struck a deal to secure Senator Lambie's vote.

Instead, Senator Cormann said Senator Lambie had been persuaded through classified briefings.

"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.

Prime Minister Scott Morrison chose his words carefully when asked about the prospective 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: "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."