Despite reports of clashes with police, ACT Policing Commander of Operations Linda Champion advised protesters were generally well behaved.

No arrests had been made at Government House on Monday morning, Commander Champion said.

"We're putting every resource we can towards these protesters and their activities throughout the week," she said.

"We are like the society here and the Canberrans and we do want this protest activity to end peacefully."

Commander Champion said on Sunday a protester struck a traffic controller with a vehicle after being advised to stop.

The traffic controller was taken to hospital for minor injuries and the driver of the vehicle was arrested.

Two people were also arrested on the roads on Monday for causing disruptions.

Police issued a warning to the public to expect further delays on Canberra roads this week, with protest activity likely to increase in coming days.

"We are expecting activity tomorrow [Tuesday] around Canberra, predominantly at Parliament House," Commander Champion said.

"We're asking Canberrans to plan their trips into town tomorrow and if they need to get to locations where protesters may be please allow for additional travel time."

Anti-vaccination mandate and sovereign citizen protesters targeted Government House on Monday, heckling police after they removed a Eureka Stockade flag raised.

With shopping centres and pubs targeted across the weekend, police have warned the wide range of protest groups might mean other areas of Canberra will be targeted.

Commander Champion urged Canberrans not to take matters into their own hands.

"Please call police if you think your safety is an issue. If it's life threatening triple zero, otherwise 131 444. We are here to do our job," she said.

"Those responsible will be held to account."

The convoy has travelled up and down Northbourne Avenue throughout the day, flying a range of flags and shouting mixed messages.

Protesters have since gathered at the ABC studios in Dickson.

Our journalists work hard to provide local, up-to-date news to the community. This is how you can continue to access our trusted content: