It is critical that the federal government continues to move away from a hospital-based health system by "re-empowering" general practice, the nation's peak body representing 110 general practices says.

That's despite serious concerns from GPs relating to increased workloads under a new super clinic system.

More than 100 doctors in western Sydney are cancelling surgery for the day so they can discuss the federal government's plan to establish GP super clinics.

Some GPs are flying in from Queensland and Victoria while others will be taking part via a webcast of the meeting on the internet.

"Central clinics inevitably will become more bureaucratic , they'll probably end up like a big sort of casualty ... where people just come and they don't have any ongoing relationship (with their doctor)," GP Adrian Sheen told ABC radio.

But Dr Emil Djakic from the Australian General Practice Network doesn't appear to be as concerned about the moves to establish super clinics.

"It is absolutely critical that the Australian government continue to work towards reorientating away from a very hospital-focused health care system and funding to re-empowering general practice," Dr Djakic, the network's president told ABC radio.

Health Minister Nicola Roxon conceded that under the super clinics system, a team of doctors may be working for a long period of time.

But they would not be required to invest large amounts of money on their own clinic if they don't wish to stay in one location for 30-40 years, she said.

The federal government made an election promise to build 31 clinics, but ABC radio says that number has now increased to 36.