Unmasked protesters marched from Sydney’s Victoria Park to Town Hall in the central business district, carrying signs calling for “freedom” and “the truth”.
There was a heavy police presence, including mounted police and riot officers, in response to what authorities said was unauthorised protest activity.
Police arrested 57 people, with more under investigation, after crowds broke through barriers and threw plastic bottles and plants. They face hefty fines and penalties.
New South Wales Police said it supported the rights of free speech and peaceful assembly, but the protest was a breach of public health orders.
“The priority for NSW Police is always the safety of the wider community,” the force said in a statement.
Brad Hazzard, the state’s health minister, said: “We live in a democracy, and normally I am certainly one who supports people’s rights to protest ... but at the present time, we’ve got cases going through the roof and we have people thinking that’s OK to get out there and possibly be close to each other at a demonstration.”
David Elliott, the New South Wales police minister, said: “You don’t have to be an epidemiologist to work out that if this is a superspreader event, we can forget about lifting restrictions next week.”
The protest came as the number of Covid-19 cases in the state reached another record, with 163 new infections in the last 24 hours.
Officials fear the outbreak could jeopardise the rest of the country.
Greater Sydney has been locked down for the past four weeks, with residents only able to leave home with a reasonable excuse.
Of the new cases, at least 45 had spent time in the community while infectious, health authorities said. That figure is being closely watched as the state considers whether to extend the lockdown, which is due to end on 30 July.
Meanwhile, in Melbourne, thousands of unmasked protesters marched downtown chanting “freedom”. Some lit flares as they gathered outside Victoria state’s Parliament House.
They held banners, including one that read: “This is not about a virus it’s about total government control of the people.”
Police arrested six people in the city, including one for assaulting an emergency worker, and fined dozens of others for failing to comply with orders to stay within 5km of home.
Victoria, which includes Melbourne, reported 12 locally acquired Covid cases on Saturday, down from 14 a day earlier, in what Martin Foley, the state’s health minister, called a reassuring sign for the country’s second most populated state.
Other protests took place in Brisbane, where there are no restrictions, and a car rally is planned in Adelaide, which is also under lockdown. Police warned they will make arrests over unlawful activity.
“We’ve turned the corner, we’ve got it sorted. We’re hitting the marks that we need to make; a million doses a week are now being delivered,” prime minister Scott Morrison said.
“We are well on our way to where we want to be by the end of the year and potentially sooner than that.”
The federal government said it would send 50,000 extra Pfizer doses to Sydney, and adults in Australia’s largest city are being urged to “strongly consider” AstraZeneca because of the scarcity of Pfizer supplies.
Despite its struggle with spikes of infections, mostly of the Delta variant, Australia has managed to keep its epidemic largely under control with a total of about 32,600 cases and 916 deaths.
Additional reporting by agencies