Mounted police used pepper spray in Melbourne to break up crowds surging toward police lines, while smaller groups of protesters were prevented from congregating in Sydney by a large contingent of riot police.
There was no information immediately available on arrests. Police in Victoria had vowed to hand out fines of A$5,000 ($3,600) to any protestor they could identify taking part.
Sydney, a city of more than 5 million people, has been in a strict lockdown for more than two months now, failing so far to contain an outbreak that has spread across internal borders and as far as neighboring New Zealand.
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The vast majority of the 894 cases reported across Australia on Saturday were found in Sydney, the epicenter of the Delta variant-fueled outbreak.
"We are in a very serious situation here in New South Wales," state Health Minister Brad Hazzard said. "There is no time now to be selfish, it's time to think of the broader community and your families."
Police patrolled Sydney's streets and blocked both private and public transport into the center of the city to reduce the number of people gathering at an unauthorized protest.
In Melbourne, a large crowd managed to march through the city, with some protesters clashing with police, after state Premier Daniel Andrews expanded a lockdown in that city to entire state.
Victoria Police Chief Commissioner Shane Patton had earlier warned people to stay away from the protest, adding it was "just ridiculous to think that people would be so selfish and come and do this."
Several hundred people also protested peacefully in Brisbane, which is not in lockdown.
Although often violent, anti-lockdown protests are not broadly supported by Australians. A late-July poll by market research firm Utting Research showed that only 7% of people support the demonstrations.
Compliance with public health rules has been one of the key cited reasons behind Australia's success in managing the pandemic. But the country has been struggling to rein in the third wave of infections that began in Sydney in mid-June.
Only about a third of Australians aged 16 and above have been fully vaccinated, according to federal health ministry data released on Saturday.
New South Wales officials reported three deaths and 516 people in hospital on Saturday. Of the 85 people in intensive care, 76 were unvaccinated, officials said.
At least 96 people were active in the community during their infectious period, and there were a number of breaches of public health orders, all slowing the efforts to curtail the outbreak.
In Victoria, at least 39 people were active in the community while infectious. Eighteen people were in hospital, eight in intensive care and six on ventilators.
Australia's Covid-19 numbers are still relatively low compared to other developed countries, with just over 43,000 cases and 978 deaths.