Mr Perrottet's government suffered mixed results at this weekend's by-elections and looks set to lose the seat of Bega to Labor for the first time.
"Ultimately in a pandemic or in any situation like the one we found ourselves in you have got to make sure you are always doing what's right," he said.
Federal minister Keith Pitt agrees with the prime minister that the thousands of protesters that surrounded Parliament House in Canberra on Saturday over vaccine mandates are attacking the wrong place.
Scott Morrison insists the Commonwealth government has only ever supported mandates that relate to aged care workers, disability workers and those who are working in high risk situations in the health system.
All other mandates have been imposed unilaterally by state governments.
Mr Pitt agrees and says while everyone is entitled to protest as their democratic right, in this case it was misdirected.
"These are the decisions of the premiers, it's not the federal government that is making these decisions, these are state-based decisions," he told Sky News' Sunday Agenda program.
"They vary all over the country, There is so many decisions being taken, there is a lot of confusion around it."
But Deputy Opposition Leader in the Senate Kristina Keneally said it was the prime minister who set up the national cabinet and was prepared to take all the credit when the premiers took their measures.
"As soon as a group of protesters walks into town critical of some of those decisions, he points the fingers at the premiers, says 'it's not my fault, it's theirs'," Senator Keneally told ABC's Insiders program.
"He should stand up and condemn the violent extremists who are part of that protest. And he should make clear that has no place in Australian democracy."
ACT police want the protesters out of the campsite where they have congregated over the past couple of weeks by Sunday so the territory's iconic Canberra Show can be set up.
Meanwhile, NSW has reported 6686 new COVID-19 cases, the lowest number this year, along with 22 virus-related deaths.
Victoria announced 7223 infections and 18 deaths, while there were 7311 cases and four deaths in Queensland.
In the ACT there were 458 cases, 38 in Western Australia and 371 in Tasmania. No deaths were reported in these three jurisdictions.
Victorian Premier Daniel Andrews is considering the future of QR code check-ins in his state with other jurisdictions having ended them, albeit with some exceptions.
"We hope to make some announcements quite soon," the premier told reporters on Sunday.
"Now that we've hit the peak of Omicron, now those cases are coming down, we do have some room to make some refinements and adjustments."
