More than 200 people have since been fined.
When asked whether he felt police were justified in using non-lethal weapons, including pepper bullets, which were used at a rally for the first time on Saturday, Mr Patton said “absolutely”.
He said the vast majority of violent protesters appeared to be “angry men” aged between 25 and 40 who “came with the intent to cause trouble … and to confront police”, and his officers acted appropriately to de-escalate the situation.
“They defended themselves, they took the necessary action,” he said.
“[Protesters] came armed. That’s not protesting about freedom, that’s criminal activity.”
The Chief Commissioner said he was investigating whether public transport, including ride-share services and trams, could be shut in the lead-up to future protests to prevent large numbers of people taking part.
“To shut down the transport network to prevent people coming in … that’s a huge call, but it’s one that we’re now going to seriously entertain on the next occasion,” he said.
Police Association secretary Wayne Gatt joined Mr Patton in supporting the work of the 700 police who attended the protest, and said the use of force was necessary.
Mr Gatt said he had spoken to some injured officers, who said they were met with “overwhelming violence”
“When you’re confronted by the scenes … where people are throwing burning objects at police … you can understand why they had to resort to that use of force,” he told 3AW.
On Saturday, it was revealed organisers had billed the protest as peaceful before it went ahead and had urged followers to avoid violence, with a mix of young and old people, including children and families, attending.
But clashes with police broke out at a couple of points, notably outside State Parliament and Flinders Street Station, where police were seen using capsicum spray and non-lethal pellets on the crowd. Police said they arrested 218 people.
They said all those arrested would be fined $5452 for breaching the Chief Health Officer’s directions, totalling more than $1.18 million in fines. Officers also issued an additional 236 fines.
On Sunday, Mr Patton said a further 130 people were fined for lockdown breaches across the state in the preceding 24 hours, including an “alarming escalation” in private gatherings at homes in both metropolitan Melbourne and regional Victoria.
At least 55 fines, he said, were given to people at private gatherings, including 16 people caught at a party in Warrnambool in the state’s south-west and people at a gambling party in the Docklands.
Some 3000 calls to the Police Assistance Line were logged from Victorians reporting others for lockdown breaches.
Mr Patton said the investigation into an illegal engagement party that prompted a night curfew for Melbourne residents was continuing, with 48 fines now issued totalling more than $260,000.
They include the newly engaged couple and the bride-to-be’s parents who hosted the party during lockdown restrictions.
A further eight attendees, he said, were still to be interviewed.
Mr Patton said there were 1600 police officers working on COVID-19-related duties including border watch, hotel quarantine and patrols.
“What my members have been asked to do over a lengthy period of time is quite astonishing. I’m tremendously concerned about the toll it’s taking on Victoria Police.
“But that’s the role we signed up for … to protect the public.”
Victoria recorded 65 new local cases in the 24 hours to Sunday.
The numbers on Monday are expected to include a spread from the Shepparton cluster to Mansfield. A person with symptoms went to the emergency department at Mansfield District Hospital on Saturday night.
Health authorities are also expecting more cases to emerge from the Royal Melbourne Hospital outbreak in coming days.
Deputy secretary of COVID response Kate Matson urged anyone with symptoms to get tested.
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