Adults aged 59 and under will now be offered Pfizer's vaccine based on the updated advice, reports Xinhua news agency.
"The experts at ATAGI have today updated their advice to recommend the Pfizer vaccine be preferred for adults aged 59 and under," Hunt said in a statement.
"The ATAGI advice remains clear that the AstraZeneca vaccine is highly effective in preventing severe disease caused by Covid.
"This updated advice received today is based on new evidence demonstrating a higher risk for the very rare TTS (thrombocytopenia syndrome) condition in the 50-59 year-old age group," he added.
According to the minister, AstraZeneca remains recommended for those aged 60 and over based on the much higher risk of illness and death from Covid in this age group, and the lower risk of this condition.
Despite the change, Hunt said the rollout was on track and that every Australian who wants to be vaccinated will receive at least their first dose by the end of 2021.
The ATAGI's decision came after 12 new cases of "this rare, but sometimes very serious clotting condition" were identified in the last week.
Chief Medical Officer Paul Kelly said the medical advice was that people who received their first AstraZeneca dose without any adverse effects should get their second dose.
"Anyone who has had a first dose of AstraZeneca without a problem should feel very confident to have their second dose," he said.