The Australian Medical Association has voiced safety concerns, saying it's "a second-best option" for patients, and further reduces regular consults with patients, particularly men.

It will be the second winter the influenza vaccine has been administered to adults at ACT pharmacies.

AMA vice president Dr Tony Bartone urged the public to think about their circumstances before having a pharmacy-administered vaccination, saying in a quest for convenience patients may lose out.

"It is about ensuring the best possible standard of care is applied rather than an acceptable or passable standard of care," he said.

Patients shifting away from a medical practice may feel as though they are getting a bargain but Dr Bartone said the move reduced opportunity across the country for consultation and valuable preventative care.

. "If there was an adverse reaction in the retail space it would be challenging at best and very problematic at worst," he said.

"It is an extremely safe process but we run the risk of overlooking and over-simplifying something that does carry a very low but inherent risk."

Pharmacies in Canberra are offering the flu shots for between $10- $15 dollars and Dr Bartone questioned whether the low-cost offering was part of a more generalised marketing push in the larger discount stores.

"I don't even think it can be supplied into a practice at the price that it is being offered," Dr Bartone said.

He also reminded the public to check if they were eligible to be dosed for free such as those over 65, pregnant women, Aboriginal and Torres Strait Islander people 15 years and over and those older than six months with underlying medical conditions which predispose them to complications due to flu.

ACT Pharmacist Ben Jackson had customers relay stories about pharmacists in discount chains jumping over the counter to give flu shots.

In his store customers were given privacy in one of two treatment rooms, were being dosed with the quadrivalent (four strain) vaccine, were thoroughly checked by through a questionnaire and had the support of a nearby medical centre in case of any adverse affects.

"If I was in a smaller corner store pharmacy I wouldn't do it," he said.

"One you want privacy but two you have to be equipped ready to go in case if there is a reaction you have to have space and room for them to lie down if they need."

He understood the AMA's concern about encouraging people, particularly men, to have regular health checks.

Mr Jackson felt it was a common goal and why his pharmacy did health awareness campaigns and provided extra services for wound care, sleep apnoea, diabetes, smoking cessation and medication management.

National Health Coop general manager Blake Wilson, who oversees eight medical clinics, supported broader access to flu vaccination as it had proven public health benefit.

"From an individual perspective if they don't have it and don't get sick they are lucky to have a good immune system or they are relying on herd immunity where lots of other people have had the flu vac and therefore it doesn't spread as much when there aren't as many carriers," he said.

People with certain conditions should steer clear of the vaccine and while these would be flagged in a pre-vaccination questionnaire in a pharmacy setting, he said without regular contact with a doctor people ran the risk of not being well informed about their own health.

"There is always benefits to speaking with a doctor and making sure you are getting considered medical advice whenever you are taking any medication," he said.

"It's increased availability can be a very good thing. Naturally you have got to make sure that the continuity of care is provided and they are in a safe space but many pharmacies do a wonderful job at that."