The Immigration Department told the independent health provider on Christmas Island not to publish a report that showed alarming rates of mental health issues among children in detention, an inquiry has heard.

During the third hearing of the inquiry into children in detention, Dr Peter Young revealed that the department had explicitly told International Health and Medical Services not to publish a report showing children in detention suffered very high levels of mental illness because of the harsh environment.

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Inquiry hears evidence of neglect

Experts expressed concern about the level of medical care at an inquiry into children in detention, reports immigration correspondent Sarah Whyte.

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Dr Young, a psychiatrist and former medical director, visited Christmas Island three times.

"[The results] are very concerning. It's quite clear that a large number of children have significant distress," he said.

Dr Young said the results were reported to the Immigration Department in recent weeks and they were then asked to be withdrawn.

"The department has been very negative towards the results . . . They are concerned about what the figures are showing,'' he said.

"They have asked us to withdraw the figures from the reporting.''

Department head Martin Bowles was later asked about the claim in the inquiry and said he was not present when it allegedly happened.

''You have heard one side of the statement. Our normal practice is to consider these things. If our staff did an inappopriate thing, then I will deal with that,'' he said.

Dr Young then told the Australian Human Rights Commission inquiry that he found it "troubling" the number of times the Immigration Department had overruled decisions made by medical experts.

Children stripped of basic medications

Two doctors who worked on the island also gave evidence of the treatment of asylum seeker children who arrived on Christmas Island during 2013.

In one instance a three-year-old girl who had epilepsy had her documents and medication taken off her when she arrived, only to then suffer seizures.

Dr Grant Ferguson said the girl was eventually given the same medication from the department, but after months of waiting.

''We eventually got supply of that medication she arrived with, but they only ordered a month's worth so in a few weeks time they ran out and she was back to one (medication) again, and this whole time she was having seizures," he said.

Another young boy had his hearing aids confiscated when he arrived at Christmas Island, forcing him to lip read a dialect he did not understand. Dr Ferguson said it made the boy feel very isolated and eventually he started self harming.

Another doctor, Dr John Paul Sanggaran, said stripping asylum seekers of basic medications was a major problem.

''One of the more concerning, systematic things I saw was a couple of nurses standing around a garbage bin popping pills from a boat of new arrivals straight into the bin, with no records being taken of whose medication they were," he said.

Immigration department 'smothered in secrecy'

The latest hearing comes as Immigration Minister Scott Morrison told the ABC on Wednesday night that claims of sick children and suicidal mothers made by Australian Human Rights Commission president Professor Gillian Triggs were "sensational".

"I don't think there is evidence of the claim that the high – the Human Rights Commissioner has made in the way that she has made it," he told the ABC's 7.30.

"These are difficult environments and appropriate care is provided by our people. I think they're quite sensational claims that have been made. She herself is not a doctor and we have medical people who are there who provide that care on a daily basis."

Professor Gillian Triggs responded, saying the Immigration Department was "smothered in secrecy".

''I'm basing my views on the evidence as you'd expect a lawyer to do,'' Professor Triggs told reporters in Sydney on Thursday.

The inquiry continues.

with AAP

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