Doctors at the hospital are concerned about the welfare of their dozens of patients and say it would be unethical to discharge them to unsafe conditions that could compromise their health.

"I'm extremely proud to be the health minister in a state where its doctors and nurses are putting the interest of children first," Ms Hennessy said on Sunday.

"If the staff of the Royal Children's Hospital come to the clinical view that it is not in the interests of those children to go back into detention, then we will support them."

Ms Hennessy said she was confident the doctors were motivated by concern for their patients' welfare and not by politics.

"I can only imagine what it's like to be a clinician, to treat a child, then have to reflect upon the health consequences of putting that child back into detention," she said.

Fairfax Media understands there are not currently any asylum seekers who are inpatients at the Royal Children's Hospital.

Defying new federal laws threatening two years' jail for health workers who speak out against immigration detention centre conditions, more than 400 of the hospital's doctors stood together on Friday demanding children be released from detention.

"We see a whole range of physical, mental, emotional and social disturbances that are really severe and we have no hope of improving these things when we have to discharge our patients back into detention," one paediatrician told News Corp.

The outlet reported that it understood the issue was sparked by a month-long standoff between doctors and authorities over the release of a child with a range of health issues this year.

Staff have also been outraged at immigration guards placed at the entrances of some patients' rooms for 24 hours a day.

The Australian Medical Association said it had a "fundamental problem" that children were in detention and had been asking governments to look for "any alternative" to it for years.

"We acknowledge the evidence that children in detention face circumstances which are very harmful to their health, their growth and their development," vice president Stephen Parnis said.

He said that if children did need to be detained, then they should be released "in weeks" at the absolute most.

Dr Parnis said the AMA was aware that a "number" of doctors who had provided care to children in detention had been quite distressed.

Children were presenting having self-harmed, with anxiety, severe depression and not growing in a healthy or normal way, he said.

Dr Parnis said doctors were constrained in the care that could be offered to these children.

"It flies in the face of our ethical obligation to provide good care."

The Royal Australian College of Physicians, which has long opposed children in detention, on Sunday said it supported the stance taken by Royal Children's Hospital staff.

"Detention centres are no place for children," said college president laureate Professor Nick Talley. "The health and wellbeing of children should never be open to compromise...No child should be held in detention."

Sydney paediatrician David Isaacs, who runs the children's refugee clinic at the Children's Hospital at Westmead, also backed the Royal Children's Hospital staff.

He said results of a survey of paediatricians, published in the Medical Journal of Australia, showed 85 per cent of respondents were against children being placed in detention.

Dr Isaacs visited Nauru in December 2014 and saw a six-year-old girl try to hang herself. He said his visit to the island left him deeply troubled and he experienced nightmares on his return.

"These are very traumatic cases where children are severely suicidal and in a lot of trouble," Dr Isaacs said.

However Dr Isaacs said there were many other children in detention who were not admitted but treated as outpatients. One regular patient he diagnosed with tuberculosis on Nauru is now detained in Sydney's Villawood Detention Centre. When the child comes to his clinic for treatment he and his parents are accompanied by a guard.

"That is treating them like criminals rather than patients," he said.

Immigration Minister Peter Dutton said he understood the doctors' concerns but did not support a change in government policy.

"The Defence and Border Force staff on our vessels who were pulling dead kids out of the water don't want the boats to restart," he said.

It was reported dozens of asylum seeker children have been taken to the hospital in the past year, with most in detention for between 18 months and two years.

Royal Children's Hospital chairman Rob Knowles told News Corp he supported the doctors' stand to protect the health and safety of children.

"The work of RCH doctors and nurses is highly valued by the Victorian community, and has made this hospital a global leader in adolescent and child health," he said.

"It is not surprising these same specialists would be concerned about the detention of children, on the basis that detention can have severe detrimental impacts on children's health.

"Our staff have consistently acted responsibly and in a considered manner in relation to the treatment of children in detention, and I support their right to have a responsible, considered opinion on this significant matter of public interest."