Qualified GPs said the high fail rate indicated there was either a problem with the examination or a problem with the training.

Former Australian Medical Association president Mukesh Haikerwal​ said the RACGP risked ceding control of training its junior workforce to private companies or universities if the federal government thought it was inadequate to the task.

"In the manufacturing industry, the rule is that you expect 80 per cent of your product to be fit for market," Dr Haikerwal said. "It's exactly the same here. If you're spending that much money into your training you'd want at least an 80 per cent pass rate.

"We do have to make sure that the processes are robust and there's transparency because there's a danger that what is a good system will be taken away from the colleges, which would be a disaster," he said.

The federal government increased its training places by 1200 to 1500 in the 2014 budget to respond to a shortage of GPs in some parts of Australia.