Most immediately, this means those younger health and aged care workers who have not yet been vaccinated will be offered the Pfizer shot. This may involve delays.

These people are in the cohort currently being vaccinated, together with over 70s who are unaffected by the new advice, which went to the government on Thursday evening.

Scott Morrison said the later stages of the rollout will now urgently be re-examined and re-calibrated. He said it was "far too early" to say what impact it would have on the rollout's timetable.

The government's deadline for all eligible people who want a vaccine to receive at least one shot by the end of October is set to blow out.

Vaccine purchases will also be reviewed.

Morrison unveiled the advice from the Australian Technical Advisory Group on Immunisation at a hastily summoned press conference on Thursday night, also attended by Health Minister Greg Hunt, Chief Medical Officer Paul Kelly, and Health Department Secretary Brendan Murphy.

Morrison said he had received the advice "in the last 15 minutes".

The government had urgently sought the advice following evidence overseas of a link between the AstraZeneca vaccine and blood clots, with some deaths resulting.

There has been one clot case in Australia, a man in his 40s.

Explaining that the Pfizer vaccine should be preferred over AstraZenica for those under 50s, ATAGI said, "This recommendation is based on the increasing risk of severe outcomes from COVID-19 in older adults (and hence a higher benefit from vaccination) and a potentially increased risk of thrombosis with thrombocytopenia following AstraZeneca vaccine in those under 50 years".

But it said AstraZeneca can be used in adults under 50 "where the benefits clearly outweigh the risk for that individual and the person has made an informed decision based on an understanding of the risks and benefits."

Under 50s who've already had one AstraZeneca dose without serious adverse effects can be given a second dose, the advice said.

ATAGI described the possible blood clot side effect as "rare but serious".

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Advice is being provided to GPs involved in the rollout.

This is the latest difficulty to hit the rollout. The government this week stressed the main problem was shortage of supply, with AstraZeneca doses from Europe being held back and CLS, which is manufacturing the vaccine locally, not gearing up to the one million weekly target as fast as expected.

As of Thursday, one million doses of one or other of the two vaccines had been administered in Australia. At present Australia only has the two vaccines available.

Morrison stressed that decisions were up to individuals and their doctors - this was advice only.

"There is not a prohibition on the use of the AstraZeneca vaccine for persons under 50. There is an expression of a preference."

Kelly said a clot was very rare. "At the moment, it seems to be around four to six per million doses of vaccine. It's only been found in the first dose of the AstraZeneca vaccine, usually within four to 10 days after that vaccine. But it is serious, and it can cause up to a 25% death rate when it occurs."

In a late night statement AstraZeneca said it respected the government's decision based on advice to recommend AstraZeneca's vaccine be used in those over 50.

It noted that, "Overall, regulatory agencies have reaffirmed the vaccine offers a high-level of protection against all severities of COVID-19 and that these benefits continue to far outweigh the risks".