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 there are currently 13 active cases in the state.
People in Australia must stay at least 1.5 metres away from others.
Please check the relevant guidelines for your state or territory: NSW, Victoria, Queensland, Western Australia, South Australia, Northern Territory, ACT, Tasmania.
If you are experiencing cold or flu symptoms, stay home and arrange a test by calling your doctor or contact the Coronavirus Health Information Hotline on 1800 020 080. News and information is available in 63 languages at sbs.com.au/coronavirus.
