Scott Morrison says he respects the decisions of state and territory leaders to shut their borders but understands why people have been left frustrated.
Travellers heading from NSW to Victoria have been caught up in traffic bottlenecks as they try to cross the border before the southern state locks out its northern neighbour from midnight on Friday.
There have been several border changes in recent days in response to COVID-19 clusters in Sydney and Melbourne.
"As much as we would like there to be greater consistency across all of these things, we must respect (the states') jurisdictional authority," Mr Morrison told reporters on Friday.
"They are ultimately responsible for what would happen in their state if there were to be an outbreak in their state.
"As prime minister, I do respect that."
Western Australia has re-established its hard border with Victoria, which recorded two new cases on Friday reportedly linked to an eight-strong outbreak.
The rise in Sydney cases prompted the Northern Territory to revise its public health orders on Thursday and bar entry for all greater Sydney residents
South Australia has also re-established its hard border with NSW, along with a 100-kilometre buffer for border communities.
Mr Morrison urged states to balance the risks of COVID-19 transmission with disruptions caused to people.
Queues of vehicles have formed in southern NSW as Victorians try to return home and avoid a mandatory two weeks in quarantine for arrivals after midnight on Friday.
"I understand the frustrations people have with the disruption," Mr Morrison said.
Mr Morrison has previously hit out at some states for their border management, criticising WA's decision to shut last year as "economic protectionism".
The federal government had aimed for Australia to be fully open by Christmas, a plan dashed by the COVID-19 outbreak on Sydney's northern beaches.
Victoria's two new cases are understood to be among 170 close contacts of eight cases linked to a bayside Thai restaurant.
The two people left Victoria on December 30 and travelled to the south coast, visiting a hotel and cafe before being tested in NSW.
They then returned to Victoria.
They are not yet officially counted in the state's community transmission case numbers, which remain at eight.
NSW reported three new cases of community transmission on Friday, all linked to western Sydney.
None of them are related to the northern beaches hotspot, which is now up to 146 cases after two previously recorded infections were linked.
Queensland started the year with a day of no new cases and has 13 active cases but one of those has been identified as the second case in the state of a fast-spreading South African variant of the virus.
Queensland Chief Health Officer Jeannette Young said the man in his 50s had travelled from South Africa, the UK and Qatar, and was now in hospital.
She said routine testing had returned positive results for viral fragments in wastewater at treatment plants at Bundaberg in Wide Bay and Elanora on the Gold Coast.
Dr Young urged people in those areas to come forward for testing with even the mildest of symptoms so cases could be detected to prevent further transmission.