AMA president Brian Owler has dismissed Joe Hockey's "personal attack", saying the government had a siege mentality and should focus on the policy.

Prime Minister Tony Abbott's funding of a new medical school in Western Australia has sparked a stoush with the AMA, which says it won't help the state's doctor shortage.

The Curtin Medical School in Midland, about 20km northeast of Perth, will cater for 60 students by 2017 and 110 a year by 2022.

AMA President Brian Owler raised the federal government's ire by calling it "a calamitous captain's call by Captain Chaos" because it failed to address the existing training bottleneck.

Treasurer Joe Hockey fired back, labelling Dr Owler's comments extreme, out of order, and "certainly not fitting for someone representing a great profession".

Shadow treasurer Chris Bowen quickly called on Mr Hockey to apologise for his "extraordinary" personal attack on one of Australia's most respected neurosurgeons.

The remarks proved the treasurer had a glass jaw and was incapable of taking criticism, Mr Bowen said.

Dr Owler admits he had used "colourful language" but said the focus should be on policy.

"If he (Mr Hockey) wants to make that personal, well then that's too bad," he said.

The issue was not the number of medical students but the bottleneck caused by a lack of trainee positions in WA, with a shortfall of 84 GP training places last year, he said.

"(We) need to make sure we train those medical graduates to become the GPs and specialists that this country needs."

Dr Owler also pointed to "a siege mentality here where people are accused of being members of the opposition political party any time they disagree with the government."

AMA WA President Michael Gannon said graduates were already having difficulty getting jobs.

"This was a closed, back room decision done without any consultation with people who know what this means," he said.

Mr Abbott defended the medical school that will cost the government $20 million once fully operational, saying it will help to address WA's shortage of about 1,000 doctors
compared to other states.

"Western Australia needs more local doctors," he told reporters on Sunday.

Premier Colin Barnett said the school would bring prestige to the eastern suburbs, which had felt a "little bit left behind".

"It's long, long overdue that the eastern suburbs had tertiary education available," Mr Barnett said.

The Curtin Medical School will open in 2017 and offer a five-year undergraduate medical degree.