The Australian Medical Association is urging people to hold off getting this year's flu vaccine, saying some pharmacies are offering the vaccinations too early.

Some well-known pharmacy chains are currently advertising vaccinations referencing last year's deadly influenza outbreak in parts of the country.

The AMA's national president Michael Gannon said the timing of the flu shot was important.

"We are concerned when pharmacies are out there advertising early flu shots at a time that might not be clinically appropriate," he said.

"People who are vaccinated too early in autumn might have lost protection by late in the spring when the virus has mutated.

AMA president Michael Gannon said people should hold off until May or June to get their flu shots. ( ABC News: James Carmody )

"Doctors are working closely with the Health Department in Canberra on this year's seasonal vaccination program, trying to get the best possible value out of the huge investment and to protect as many vulnerable populations as possible."

He said part of those discussions were about when exactly the vaccine should be released.

"Remember why you need to have a vaccine every year is the influenza virus rapidly and quickly mutates. It will be appropriate for some patients to defer having their flu shot until well into April," he said.

Dr Gannon said people should speak to their GP about the best time to get the flu shot.

"And it's simply not acceptable that pharmacies are deriving a fee for those populations that are entitled to free influenza vaccination," he said.

"So that's people over the age of 65, that's some groups of children, people with chronic disease, pregnant women, Aboriginal and Torres Strait Islanders."

He said the AMA welcomed any positive promotion of vaccination — but it needed to be responsible.

"We just want the retail pharmacies to be every bit as professional as GPs are and indeed those employers who organise free vaccinations for their staff," he said.