In Melbourne, mounted officers used pepper spray when elements of a 4,000-strong rally broke through police lines.
Police arrested 218 people, and at least seven officers were injured.
In Sydney, where lockdown measures have been extended for another month, more than 1,000 officers dispersed protests.
It came as the state of New South Wales (NSW), of which Sydney is the capital, recorded 825 new locally-acquired cases, the highest number for any Australian territory in a 24-hour period.
