Australia's peak medical bodies are alarmed by evidence doctors are being forced to compromise clinical and ethical standards and put their patients' health at risk as they struggle to deliver basic care to traumatised children.

The Royal Australian College of General Practitioners (RACGP), the Royal Australian College of Physicians (RACP) and the Australian Medical Association (AMA) have slammed a reported Immigration Department cover up of data showing the extent of mental health concerns among young detainees.

They say the issue is being ignored because it is happening out of the public eye in immigration detention centres.

In testimony to the Human Rights Commission inquiry into children in immigration detention on Thursday, psychiatrist Peter Young said in recent weeks the Immigration Department instructed him to withdraw data showing elevated mental health issues among the children and young people in the centres on Christmas Island and Nauru.

Dr Young was the director of mental health services at detention centre service provider International Health and Mental Services (IHMS) for three years until earlier last month.

"If we were seeing this on mainland Australia, in our community, it would be absolutely not accepted - questions would be asked immediately, social services would be involved, litigation would be involved," RACGP's chair of refugee heath Dr Christine Boyce said.

RACP president Professor Nicholas Talley said the allegation reinforced the view of the college and other peak medical bodies that the Federal Government's decision in December to disband the independent advisory body that used to have oversight of healthcare provision in the detention facilities was unjustified and detrimental.

"I am alarmed at the evidence from Dr Peter Young that the Federal Government requested figures showing the true extent of these mental health concerns be suppressed," Professor Talley said.

RACP paediatrician Associate Professor Karen Zwi, who visited Christmas Island and gave evidence to the inquiry in May, was also horrified by the evidence about children and adolescents in detention.

"Considering the minister is their legal guardian, one must question whether he can be acting in their best interests in implementing the current policies," she said.

"The college of physicians strongly supports health care workers who are brave enough to tell the truth about what's happening to their patients and to children in their care.

"They shouldn't be put in a situation where their professional standards have to be compromised, so the organisations employing them are unfortunately placing them in a very difficult situation."

Immigration Department secretary Martin Bowles has told the inquiry that he was not aware of any cover up and if department staff had acted inappropriately, he would take action.

A spokesperson for the Immigration Minister said the Government will continue to cooperate with the inquiry.

"The Government will await the outcomes of that inquiry to be detailed and any supporting evidence in the final report," the spokesperson said.

"More importantly the Government will continue to reduce the number of children in detention as we have been doing since the day we were elected.

"More than 80 per cent of children are resident in the community either on bridging visas or under residence determinations."

Mr Morrison has agreed to appear at the inquiry at a later date.

Concerns over testimony given to inquiry

The inquiry has heard a litany of claims about doctors being pressured to breach their Codes of Conduct, then their complaints being ignored and misinformation being disseminated by those in authority.

Dr John-Paul Sanggaran, who worked on Christmas Island in October and November last year and co-authored 92 pages of complaints with 14 of his colleagues, said he was frustrated the AMA had been told IHMS's regional director Dr Mark Parrish had addressed the issues, "resolving these misunderstandings and allaying the individual doctor's main concerns".

"I think it was quite a misrepresentation of what actually occurred," Dr Sanggaran said.

He also took exception to testimony by Dr Parrish, at a previous hearing, that the detention centres complied with the RACGP guidelines for management and provision of health care.

"Centres within immigration detention are in fact self-accredited against a modified version of general practice standards developed in collaboration with DIMIA (Department of Immigration and Multicultural Affairs and Indigenous Affairs), and the RACGP does not accredit the clinics nor are they accredited by an external body," Dr Sanggaran said.

The RACGP has told the ABC it also has concerns about Dr Parrish's testimony.

"We believe that we have absolutely enough evidence to think those standards in many cases are not being met and, even if they were, the standards themselves needed to be reviewed several years ago," Dr Boyce said.

"Over the last months it's really been a concern to us that the general public haven't really been getting very good quality information and they are being kept in the dark," she said.

"It makes doctors feel really powerless to help these people, it makes us feel very angry and it makes us feel very ashamed that damage that's being done by Australia actually exceeds the damage that's been done prior to arrival - which is a fairly big call if you consider what's happened to most of these people before they've arrived in Australia.

"We are creating traumatised individuals ... we feel quite desperate, to be honest."

Do you know more? Email investigations@abc.net.au.