Extra police were deployed as hundreds of protesters gathered at Civic Hall on Sunday carrying Australian and Eureka flags, to protest against vaccine mandates and new state pandemic laws.

Ballarat Mayor Daniel Moloney told AAP that while the town is known for its historic protests, there was never a good time to disrupt local trading.

"Half of the businesses in Ballarat are closed currently, businesses have in many cases decided to close for a couple of hours," he said.

One Ballarat bottle shop posted a sign saying "We will open on Sunday after the tantrum leaves town".

The council was also forced to postpone half a dozen events planned for Sunday to commemorate the 167th anniversary of the Eureka Stockade on December 3, 1854.

On that date, about 300 British soldiers confronted gold miners protesting about restrictive laws, and about 60 people were killed.

The rally has tried to associate itself with the historic battle, with "Eureka United" flags, and the crowd taking a "Eureka Oath", but Cr Moloney said any links were somewhat tenuous.

He said he did not want people to feel nervous about attending the town's commemorations.

"We want Eureka events to be solemn occasions, we don't want any potential for a clash," Cr Maloney said.

On Saturday, up to 10,000 people also rallied in Melbourne, bringing traffic to a standstill at Flinders St station before gathering outside the ABC in Southbank and Government House.

Sunday's crowd appears to have a number of disparate concerns centred around jab mandates and pandemic laws, but there are concerns some protesters have neo-Nazi or far-right conspiracy group links.

The state government's controversial pandemic bill, which makes the premier and health minister responsible for making health orders, passed parliament on Thursday.

It will replace the existing state of emergency on December 16 and makes Victoria the first state in Australia with pandemic-specific laws.

There are currently 39 COVID-19 cases linked to mass protests in Melbourne last month, with three people hospitalised and one in intensive care.

Australian Associated Press