New AMA president Michael Gannon says the Turnbull government's freeze on the Medicare rebate to GPs is unfair and they are "at breaking point".

The new president of the Australian Medical Association has stepped straight into the political fray, siding with Labor's stance to end the six-year freeze on Medicare rebates.

"GPs are at breaking point. They can't take too many more cuts," West Australian obstetrician and gynaecologist Michael Gannon said on Sunday.

Describing the coalition's decision to extend the freeze on indexation for Medicare rebates to 2020 as "unfair and wrong", Dr Gannon said it reflected a continued underinvestment in GPs.

The WA specialist was elected head of the peak doctors' lobby group at the national conference in Canberra on Sunday, replacing outgoing president Professor Brian Owler who urged him to be "brave and courageous".

Dr Gannon said unfreezing Medicare rebates was a priority for the AMA. Labor has promised to lift the freeze at a cost of $12 billion over a decade.

"We think there's an opportunity for the coalition to change tack on this policy," Dr Gannon told reporters.

"But it should be just the start of a wider debate. Unravelling the freeze is not a solution to the underfunding of general practice. We need to do so much better."

He supports the Royal Australian College of GPs television ad campaign against the Medicare rebate freeze that starts on Sunday.

GPs offer enormous value for money and the government should stop seeing them as a cost and more of an investment in the health of the community, he said.

Earlier on Sunday, Opposition Leader Bill Shorten said he didn't blame doctors standing up for their patients.

"The frontline of our health care system is hard-working GPs, many of them small businesses," he told reporters in Canberra.

"The fact that the Turnbull government wants to freeze the rebates they receive for six years is basically putting the doctors in the worst of all possible choices."

Dr Gannon, the outgoing AMA president of WA, has previously aired concerns the AMA was becoming too left-wing.

"This job is intensely political at the best of times," he said.

"Health is at the top of the agenda, health should remain at the top of the agenda, and the AMA will make sure of that."