Doctors are set to ramp up their campaign against federal legislation that prevents them from blowing the whistle on atrocities in detention centres.

Outraged doctors unanimously passed two motions at the Australian Medical Association's national conference on Saturday calling on its policy-making federal council to push for changes to the government's policy of detaining children.

They also want the government to amend legislation that prevents them from speaking out about failures in detention centre health care.

Dr Paul Bauert, director of pediatrics at Royal Darwin Hospital, says he and his staff have ethical concerns about sending children with psychological disorders back to Nauru and other centres.

"We're in a bit of an ethical bind in that we recognise that this is causing ongoing damage and probably permanent damage to many of them," Dr Bauert said.

"They still present with identification as a boat number, they have several guards."

Dr Bauert called for an end to the detention of children and the need for doctors to identify vulnerable children in light of allegations of sexual abuse on Nauru.

He has moved a motion calling on the AMA to urgently review its policy on asylum seekers in light of evidence that permanent and ongoing damage is being inflicted on detainees.

The damage has been noted since changes to legislation in 2013 by the then Labor government, which announced asylum seekers would be processed offshore and never be resettled in Australia.

Doctors are also calling for the government to amend the Australian Border Protection Act to allow doctors to publicly disclose failures in detention health care.

Dr Richard Kidd said the legislation presents a threat to whistleblower doctors working in detention centres as they could face two years in prison if they speak out.

He said doctors had a right and a responsibility to blow the whistle.