Professor Brett Sutton says regions like the Wimmera and Grampians are being kept in the same lockdown restrictions as regional areas with active coronavirus cases for their own protection.
The state government's roadmap announced on Sunday included a plan for all of regional Victoria, meaning restrictions cannot be eased until there is a collective daily average of fewer than five cases over 14 days.
Asked on Monday why places like the Wimmera and Grampians with zero active cases could not come of lockdown earlier than others like Geelong, the chief health officer said he did not want to risk people bringing the virus to those regions.
"There is a risk of creating bubbles in regional Victoria that just drive other people to move to those settings, to go to a place where they can go to restaurants or where they might be able to go to a pub," Professor Sutton said.
READ ALL LOCAL NEWS HERE
"Cabinet has talked through this at length - I think that there was real consideration about how to make it work.
"But we're also cognisant that even if you haven't had a case for months, the movement of people for essential reasons brings a risk of seeding into any one of those places.
"If you've got different settings across regional Victoria, then that risk is heightened."
He said Geelong was doing well to bring down its coronavirus cases.
"Fingers crossed, Geelong is on exactly the same setting as the rest of Victoria," he said.