Daniel Andrews has accused Scott Morrison of using “double speak to extremists” over the Prime Minister's comments addressing recent protests in Melbourne.
But Mr Morrison has defended his response, maintaining he could not have been clearer in denouncing violent threats connected with the protest movement.
The volatile protest scenes had seen people chanting they wanted to "hang" and "kill" the Victorian Premier earlier this week and featured a prop gallows and noose.
Mr Morrison on Thursday said he condemned violent elements among protesters opposing the state's pandemic powers bill, but also recognised their frustration.
Mr Andrews on Friday described the prime minister's response as “dangerous”, accusing him of chasing votes from extremists.
“I’m not about chasing through double speak the votes of extremists or their preferences,” he told Channel Nine’s Today Show.
"If others choose to do that - that’s on them.”
Mr Morrison later defended his response, saying he had no "sympathy" for violent behaviour "whatsoever".
"I couldn't have been clearer about denouncing the violence and the threats and the intimidation," he told reporters on Friday.
"They have no place in Australia's public policy debate."
Mr Morrison also said on Thursday it was time for state governments to step back in "telling Australians what to do."
"There are many people who are feeling frustrated," he told reporters.
"It's time for governments to step back and for Australians to take their lives back."
He had raised concerns about state-imposed vaccine mandates, drawing criticism also from leaders in Queensland and Western Australia.
Labor Leader Anthony Albanese earlier said Mr Morrison had "failed to unequivocally condemn the violent and extreme" aspects of the protest through his remarks.
"It is beyond comprehension that the Prime Minister seems incapable of putting forward a clear and unequivocal condemnation of the threats without then seeking to qualify that condemnation," he told reporters.
The controversy centres on Victoria’s Pandemic Management Bill, which is aimed at replacing the current state of emergency powers in pandemic emergencies.
The Andrews government delayed debate on the pandemic laws on Thursday to give it time to make changes to secure support for the legislation.
The law gives power to the premier and to the health minister, rather than the chief health officer, to declare a pandemic for up to three months, with no outer limit.
Asked about his relationship with Mr Morrison, the Victorian premier had earlier said: “it will be a lot better when he stops double speaking to extremists.”
"It's taken too long for people just to be straight. They're sending mixed messages and that is dangerous," he said.
"I don't want anyone, whether it's people who are weak leaders or extremists, to take away from what Victorians have built and sacrificed."