Scott Morrison has rebuffed a plea from the Australian Medical Association to change policy on Nauru, and bring families and children to Australia, saying he will not “put at risk any element of Australia’s border protection policy”.

The prime minister told reporters on Thursday the government was already in the process of “getting families off Nauru” and had pursued a refugee resettlement deal with the United States to achieve that end.

But he said he had no intention of softening Australia’s border protection policy, because Labor had adjusted the deterrence regime after the election of Kevin Rudd “thinking it would have no effect, then 1,200 people died”.

“So I’m not going to do that,” he said.

Morrison’s rebuff follows a strong intervention from the AMA president, Tony Bartone. Bartone wrote to the prime minister to seek the removal of families from a situation he characterised as an “humanitarian emergency requiring urgent intervention”.

Bartone told Morrison he made the decision to write because of “a recent groundswell of concern and agitation across the AMA membership and the medical profession about conditions on Nauru, and the escalation in reports of catastrophic mental and physical health conditions being experienced by the asylum seekers, especially children”.

“There are now too many credible reports concerning the effects of long-term detention and uncertainty on the physical and mental health of asylum seekers,” Bartone said in the letter to Morrison. “It is within the power of the government to move on this issue and play its part in allowing traumatised people to begin rebuilding their lives.”

Paul Bauert, a Darwin-based paediatrician, was in parliament on Thursday lobbying MPs from all sides to try and build support for a change in policy.

Bauert has assessed medical reports for children on Nauru involved in recent court proceedings to secure medical transfers to Australia. He said he had assessed eight or nine cases in the past six weeks, and seven children were critically ill.

“I think it’s a miracle there hasn’t been a death so far,” Bauert told Guardian Australia. “There are at least another 30 children thought to be extremely unwell that need assessment by somebody like me.

“The ability to let the politicians know what’s really happening with these kids and how unwell they are, I think, has been a bit revealing to some of them.”

The deteriorating conditions on Nauru also featured during a parliamentary debate triggered by a motion of no confidence in the home affairs minister, Peter Dutton.

The motion against Dutton failed by one vote. Thursday’s debate followed a Labor-dominated Senate committee finding the minister misled the parliament in relation to the au pair controversy.

The Tasmanian independent Andrew Wilkie wondered how it was OK to intervene “on humanitarian grounds for au pairs to come to this country but not OK for the minister to intervene in numerous cases”.

Wilkie listed cases where the federal court had intervened to protect the welfare of children on Nauru, ordering transport for a 10-year-old boy who attempted suicide three times and needed surgery, and another repatriation of a young girl who attempted suicide three times.

“The federal court had to intervene in the case of a 14-year-old girl who doused herself in petrol and set herself alight on Nauru … in the case of a 17-year-old boy who suffers from psychosis and needed to be reunited with his mother,” Wilkie said.

“The federal court had to intervene in the case of an adolescent girl suffering major depression and traumatic withdrawal syndrome … in the case of a critically unwell baby … in the case of a 12-year-old boy on Nauru refusing fluid and food for nearly two weeks.

“The federal court had to intervene in the case of a 17-year-old girl on Nauru refusing all food and fluid and diagnosed with resignation syndrome … in the case of a 12-year-old girl on Nauru who has attempted suicide several times, also setting herself on fire.

“The federal court had to intervene in the case of a 14-year-old boy on Nauru, suffering major depressive disorder and severe muscle wastage after not getting out of bed for four months.

“But the minister says it’s OK to intervene in the case of two or three au pairs on humanitarian grounds when we’ve got at least 30 children on Nauru who doctors say should be brought to this country for urgent medical attention.”