The Ballarat Health Service Community Vaccination Clinic at the Mercure Hotel will start operating on Monday, vaccinating people in the highest priority 1A group before expanding to 1B and other priority groups in coming weeks.

BHS chief executive Dale Fraser said it was too early to know how the Commonwealth Government's advice to avoid AstraZeneca vaccinations for patients under the age of 50 would impact the roll-out in Ballarat.

"This site will supply both Pfizer and AstraZeneca, but having said that there's a limited supply of both," Mr Fraser said.

About 20,000 doses of vaccine are due to be delivered to Ballarat over the next few weeks. Mr Fraser said Ballarat would have a slightly larger majority of supply of Pfizer rather than AstraZeneca.

Late Thursday night the Commonwealth Government issued advice to people under 50 to avoid having the AstraZeneca jab because of the risk of developing extremely rare blood clots.

"We run both vaccines here at the moment so we have some mitigation against that immediate change but we're not quite sure what that might mean in the long run," Mr Fraser said.

Patients at the BHS CVC will not have a choice which vaccine they will receive.

"We will do a full run of Pfizer or AstraZeneca. With the cold chain storage there's an extreme clinical risk if we have two vaccines on the same day because of the different handling process required," Mr Fraser said.

"We will work through the process to understand what the AstraZeneca decision (for under 50s) may mean."

Mr Fraser said the side effects and complications associated with the vaccine were "relatively minor" given the size of the population already vaccinated globally.

"It's about risk and reward and I think that's the conversation we need to have. How much risk are we facing and therefore do those risks outweigh the perceived benefits of the vaccine.

"At this stage we believe the vaccine is our way out of this pandemic. We have survived the last 12 months with social distancing, hand washing, lockdowns and masks and have been waiting for this opportunity to have the vaccine to give us the ability to get about a normal life."

Mr Fraser said there had been no major complications from the roughly 7000 vaccinations given so far in Ballarat, with only minor side effects such as headaches and aches and pains reported.

Ballarat currently receives about 4000 to 5000 vaccines a week but Mr Fraser is confident that supply will increase over time. At its peak the BHS CVC will be able to immunise 1200 people a day and will be open up to 12 hours a day, seven days a week.

During its initial phase though it is likely to be open four or five days a week depending on the supply of vaccine.

"Our capacity is always limited to the supply of vaccine we receive," he said.

Securing enough staff to man the clinic has also been a challenge.

"Health care workers are in short supply. When this clinic is fully operational we will have the best part of 100 people involved who come from a range of areas," he said. "Over the period of the next six to seven months this will remain an ongoing challenge along with the supply of vaccine."

Mr Fraser said the Mercure was chosen as the preferred site for the Ballarat vaccination hub because it had enough undercover-roof space to account for Ballarat weather, appropriate waiting and recovery spaces, areas for preparation of vaccines, public transport links and parking.

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"It met those requirements and it was ready to go. A number of areas we considered would have taken a lot of preparation work, minor building works, and given the need to get the program going we wanted to get something fit for purpose."

The Mercure clinic will operate until at least November. It will only take patients who have booked through the Victorian Vaccine Call Centre on 1800 675 398.

"November will give us a very big impact on the population, hopefully the entire population who need to have it done," Mr Fraser said before adding the COVID-19 vaccines would still be available through other hubs, clinics, GPs and health services in Ballarat.

He urged people who had made an booking to make sure they attended their appointment.

Once thawed, the Pfizer vaccine has a shelf life of five days but once drawn in to a needle it must be used within hours.

"We encourage anybody who made a booking who can't attend to let us know. The last thing we want is to have a vaccine ready, a person ready to inject it and no one ready to receive it ... putting it back in the fridge to use tomorrow is not an option," he said.

Prime Minister Scott Morrison announced yesterday that, following the government decision to back health advice to avoid people under 50 receiving the AstraZeneca jab, that Australia had secured an additional 20 million Pfizer coronavirus vaccines, doubling the amount of doses set to arrive in the country this year.

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The Australian Medical Association commended the government for listening to medical advice on the AstraZeneca vaccine and taking a more cautious approach to the rollout, with emerging evidence there is a very low risk of clotting associated with the vaccine.

"I want to emphasise the AstraZeneca vaccine for people who are 50 and over is considered very safe and the benefits vastly outweigh any risks," said AMA President Dr Omar Khorshid.

"The clotting seen in few patients around the world is extremely rare, quite separate to normal thrombosis, and occurs at about 1 in 250,000. By comparison if you contract COVID-19 the risk of dying is much higher.

"This setback may slow down the vaccine rollout, but it also means the rollout is based on the best advice possible - it is not a race to the finish line."

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