Federal Health Minister Greg Hunt announced on Thursday that the AstraZeneca vaccine would no longer be recommended to people between 50 and 59, after the government's vaccine advisory body said new data meant the ratio of risk to benefit between the risk of blood clotting and the risk of contracting COVID-19 in that age group had changed.

The country's health experts urged people over the age of 50 who had one shot of AstraZeneca already to still get their second dose, saying the already rare risk of the blood-clotting side effect was even lower with the second dose.

The ACT government will need to be assigned an extra 60,000 doses of the Pfizer vaccine in coming months, as there are 30,000 people in the 50-59 age group that are still to be vaccinated in the territory.

There are 49,500 Canberrans aged between 50 and 59.

In a statement, Chief Minister Andrew Barr said rescheduling vaccines for those who already had an appointment for AstraZeneca but were no longer advised to get it was the government's priority.

"We are asking any ACT resident aged 50-59 years who has not yet booked a vaccine appointment to be patient while we work through these changes," he said.

"When we are in the position to open more appointments to this age group, we will let the community know. In the meantime, if you are aged 50-59 years please do not contact the COVID-19 booking line."

The ACT government was working with the federal Health Department to confirm the supply of the Pfizer vaccine it will receive in coming weeks.

It is now likely the opening of a third vaccination hub in the territory will be further delayed, with more demand on the already limited supplies of the Pfizer vaccine.

Federal health authorities said the change in advice was due to new data on the rate of the blood-clotting syndrome in people aged between 50 and 59, and was taken to be a more cautious approach.

Chief medical officer Paul Kelly said the Australian Technical Advisory Group had "balanced the risk and benefit of the vaccine in the context of where we are right now in Australia in relation to the COVID-19 pandemic".

"The benefit of AstraZeneca in the over-60s remains much higher than the risk of this particularly rare but sometimes serious syndrome," Professor Kelly said.

He reiterated the AstraZeneca vaccine was highly effective against the virus.

It's a further blow to the wider vaccine rollout, which now must rely on the overseas-manufactured Pfizer vaccine for the majority of the population.

More than 6 million vaccine doses have been administered in Australia since February.

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