The ACT government on Wednesday launched this year's campaign to get people vaccinated against flu.

Territory Health Minister Rachel Stephen-Smith said Canberrans should remember that most would be getting three shots this year: two of a COVID-19 vaccine, and one of the flu vaccine.

"You do need to leave two weeks between any COVID vaccination and your flu vaccination," she said.

"Talk to your [general practitioner] if you have any concerns at all, and if you book in for your flu vaccination with your GP, they'll probably talk to you about booking in for a COVID vaccination if you're eligible as well."

The minister said there was still a risk of COVID-19 in the Canberra community, so it was imperative people got the flu vaccine to ensure flu didn't have a significant impact on the ACT's health system.

She said the ACT and Australia had seen "incredibly low numbers" of people with the flu last year, but suggested people shouldn't become complacent given COVID restrictions had eased since then.

"Obviously, last year, we saw people social distancing, we saw people taking on those behaviours that are likely to keep viruses at bay, but we don't know what's going to happen this year," Ms Stephen-Smith said.

"Influenza is a highly contagious viral infection and can cause very serious illness.

"To better protect you and your family from the flu, it is important to be vaccinated every year."

Australian Medical Association ACT president Dr Antonio Di Dio said he was concerned that hesitancy towards COVID-19 vaccines would have an impact on flu vaccine numbers.

However, he said he'd been heartened by the response of his own patients at Yarralumla Surgery.

"We have been delighted by the fantastic response to [our flu clinics]," he said.

"[As for] my colleagues in the ACT who've started their flu clinics at their practices, again, they are reporting fantastic attendance.

"So it doesn't look like the hesitancy has extended to the flu [vaccine], which is as it should be because the flu vaccine has demonstrated itself to be an unbelievably safe vaccine year after year."

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Ms Stephen-Smith reiterated that the flu vaccine was certainly safe.

"I'd really strongly encourage people to get it as we would with the COVID vaccine - incredibly safe and incredibly effective vaccines we have in Australia," she said.

The minister said people in Canberra under 50 who had an underlying health condition would be able to start accessing the Pfizer vaccine in a few days.

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