Treasurer Joe Hockey has launched a blistering attack on Australian Medical Association president Brian Owler's "extreme" criticism of the prime minister, while defending a federal government decision to help fund a new medical school in Perth.

But Tony Abbott stopped short of endorsing his treasurer's comments, stressing he had a great deal of respect for the doctors' body and instead responding to the specific policy concerns raised by Dr Owler.

Dr Owler told Fairfax Media the decision to fund the medical school a "calamitous captain's call" because the AMA believed the country already had too many medical schools pumping out graduates who cannot find internships or specialist training places.

On Sunday, Mr Hockey said Western Australia had the fewest number of doctors per capita of any state in Australia and that the school would focus on training doctors for areas with medical representation.

But Mr Hockey said those comments were "certainly not fitting for someone representing a great profession. Quite frankly, I think his comments were out of order".