But former independent MP Kerryn Phelps blamed the Morrison government's rhetoric on asylum seekers for the spike in self-harm on Manus Island and Nauru, as doctors gave evidence about the poor health of detainees.

Mr Pezzullo told the parliament's legal and constitutional affairs committee only four of the 111 people brought to Australia under the medical transfer scheme had spent time in hospital. A further 70 were not even outpatients, Mr Pezzullo said.

"As of Friday or Thursday night not one of them was in hospital," Mr Pezzullo said.

He argued the scheme was flawed as it required the Commonwealth's chief medical officer and the minister to make a decision solely on the documents presented by two "so-called doctors" instead of contracted clinicians on the ground.

But refugee advocates gave harrowing evidence about the state some refugees were in.

An audit of the health of refugees who had applied to come to Australia under Medevac found nearly half (47 per cent) had gastroenterological problems, nearly a third (32 per cent) had suffered significant weight loss while more than one-quarter (29 per cent) had dental problems.

Eighty-two per cent suffered from depression, 38 per cent had self-harmed and 31 per cent had attempted suicide.

Dr Sara Townend said the numbers were "far worse" than other refugee camps around the world and in disadvantaged communities around Australia.

"Some of our doctors have worked in refugee camps in various parts of the world and they call us up to debrief because they say that what they are seeing in terms of the health burden is absolutely shocking and the worst thing that they have ever seen," Dr Townend said.

Asylum Seeker Resource Centre founder Kon Karapanagiotidis said a refugee on Manus Island had suffered with a prolapsed anus for four years, after he had been raped by the militia in his country.

"For four years this man was not medically treated. Four years with a prolapsed anus," Mr Karapanagiotidis said.

But Operation Sovereign Borders commander Major General Craig Furini told the committee there had been spikes in self-harm cases around the time the Medevac laws were being debated and around the federal election.

In December 2018, when the Medevac legislation was introduced, there were 66 cases of self-harm in Nauru. There were 15 cases in the same period the year before.

Then in June this year, after the Coalition won the election, there were 101 cases of self-harm on Manus Island. There had been one case of self-harm the previous June.

"We also have gained some insights in both locations but in particular Papua New Guinea that influential transferees are coaching others to self-harm in order to get to Australia," Major General Furini said.

But Dr Phelps, who led the passage of the medical transfer legislation, said the idea refugees were harming themselves to get into the country was an "outrageous assertion".

"They're not trying to make a point. They're trying to kill themselves because they've lost hope," Dr Phelps said.

"The incidents of self-harm related to declining mental health was increasing before Medevac and was one of the reasons it was needed.

"The government's rhetoric and statements around repealing the legislation triggered another level of hopelessness and a new round of self-harm and suicide attempts after the election."

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One of the lead doctors involved with the medical transfers, Dr Neela Janakiramanan, said there was no evidence there had been an increase in self-harm since the Medevac bill passed.

However Dr Janakiramanan said her group met with the Home Affairs department shortly before the May election, concerned about the impact a Liberal victory could have.

"We had identified that a Liberal win would destabilise the population of people who were overseas because of concerns an ongoing Liberal government would not progress their applications for resettlement in a timely fashion and we predicted a significant spike in mental health issues as a result of the election result, not as a result of Medevac," Dr Janakiramanan said.

Dr Janakiramanan said it was "incredibly disingenuous" for the department to say there had been a spike in self-harm due to the bill, when officials previously told their group they did not have the data.

"In our meeting with the department on the Monday after the federal election we were told by one of the deputy secretaries of the department that they didn't actually have any health information about this cohort of patients, that they couldn't comment on the health of this cohort of patients and unless we gave them access to all of the medical records for this cohort of patients and a detailed analysis of what their health concerns were, that they wouldn't be able to do anything about it," she said.

Home Affairs officials disputed this account.