Home Affairs has failed to provide evidence to support the department's concerns that asylum seekers see self-harm as the quickest way of being medically transferred to Australia.
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A Senate committee reviewed the so-called "medevac" law on Monday, with doctors, refugee advocates and lawyers arguing for the process to remain.
Passed against the government's wishes earlier this year, the laws give doctors a greater say in granting sick refugees transfers to Australia for medical treatment.
In its submission to the inquiry, the Department of Home Affairs flagged its concerns that "self-harm is perceived as the most expedient means of accessing medical transfer under the provisions".
Operation Sovereign Borders commander Craig Furini said the department had "gained insights" into the behaviour of asylum seekers offshore.
"Influential transferees - particularly those in PNG - are coaching others to self harm in order to get to Australia," Major General Furini told the committee.
But he admitted to not having evidence to support the link, agreeing instead to provide the information at a later date.
The department had also argued that incidents of self-harm increased because of the medevac bill, saying there were 15 cases of self-harm on Nauru in December 2017 compared to 66 a year later when the bill was introduced.
Major General Furini said no further analysis was done to see why asylum seekers were self-harming.
"Don't you think locking people up and torturing them for six years might actually lead to an increase in self-harm and suicidal ideation," Greens senator Nick McKim asked the officials.
As of last Thursday 111 people had been transferred under medevac but none of them were in hospital, Home Affairs secretary Mike Pezzullo said.
They are being held in detention in Brisbane, Melbourne and Sydney as the medevac legislation provides no "express return provision", he said.
Law Council of Australia argued that the legislation could be amended, rather than repealed, to include a provision that would ensure asylum seekers return offshore.
Asylum Seekers Resource Centre chief executive Kon Karapanagiotidis says the new process is helping those in need to finally access appropriate health services.
He said Home Affairs Minister Peter Dutton was arguing against the medevac laws using "lies, dishonesty and distortion".
"Let doctors be in control of life and death decisions, not politicians," he said.
Lead medical volunteer Neela Janakiramanan said acute conditions that could be easily managed in Australia had been allowed to develop into chronic ailments in Papua New Guinea and Nauru.
About 97 per cent of almost 600 refugees assessed on PNG and Nauru have at least one physical ailment, while 91 per cent suffer from mental illness.
"These numbers are far worse than among disadvantaged communities in Australia and are far worse than numbers you'd find in refugee camps around the world," Dr Janakiramanan said.
Australian Medical Association president Tony Bartone said the previous medical transfer process was "torturous" and beset by long delays.
Meanwhile, the federal opposition convened its own meeting of migration and border security experts, unions and industry groups at Parliament House.
Labor fears the country's asylum and migration system is being used by criminals and dodgy labour-hire companies to traffic exploited workers into the country.
Australian Associated Press
