The territory's Chief Health Officer Kerryn Coleman said plans have been put in place to make sure eligible Canberrans with vaccine appointments at the Garran Surge Centre from Friday were able to receive the right vaccine.

The ACT received about 3000 more doses of the Pfizer vaccine on Friday morning. As at Thursday, it had about 2000 doses of the Pfizer vaccine and 6300 doses of the AstraZeneca vaccine in its reserves.

The ACT government's vaccine hub had administered more than 12,400 doses of the Pfizer vaccine as at Thursday and more than 3400 doses of the AstraZeneca vaccine.

New advice was handed down by the country's vaccine advisory group on Thursday recommending the AstraZeneca vaccine be distributed only to those over 50.

"If they have an appointment at Garran, they will get the appropriate vaccine," Dr Coleman told ABC Radio Canberra on Friday morning.

"If they are under 50, they will be given the opportunity to be directed into receiving the Pfizer vaccine.

"We are able to manage today, but one thing today is to look at the number and stocks and supplies of vaccines to come in."

Those already booked in to get the Pfizer vaccine will be unaffected by the changes.

However, the Chief Health Officer advised anyone who had been invited to get their dose of the vaccine as part of phase 1a or 1b of the rollout to not ring up and make appointments on Friday, due to the changes from the new vaccine advice.

She said for those patients to hold off making an appointment for the vaccine until next week while the changes were worked through.

The new advice from the advisory group was made following cases of rare blood-clotting conditions among some patients in Europe and the UK who had received the AstraZeneca vaccine.

A man in his 40s from Melbourne was also hospitalised last week after he developed blood clotting and low platelet levels in the days after getting the vaccine.

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The new advice is expected to severely delay Australia's vaccine rollout, with AstraZeneca being the predominant vaccine administered in the scheme.

The federal government had previously stated every eligible Australian would be able to get a dose of the vaccine by October, although that target is now no longer expected to be met.

Dr Coleman said she was confident the vaccine program would be able to get back on track following the overnight developments.

"This is just one of a number of small barriers we have to step over in the fight against COVID," she said.

"We do come across some unusual and unanticipated side effects, and we'll be coming out with more information in coming days.

"The most important thing to understand is that [blood clotting] is a rare side effect, while it is serious, we understand that only four to six in 1 million people develop the blood clots."

Staff at ACT government run vaccine clinics have been briefed on the new advice changes before clinics opened on Friday morning.

The Chief Health Officer said officials were working with GPs and respiratory assessment clinics that were offering the vaccine as part of the rollout on the new advice, and making sure those under 50 were prioritised to get the Pfizer jab instead of the AstraZeneca.

"No medicine and no vaccine is entirely risk free, and every decision in life is a balance of risk-to-benefit," Dr Coleman said.

"Those who have had [blood clotting] concerns should talk to their GP about their own unique circumstances."

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