The "green zone" bubble between Australia and New Zealand has been suspended after new cases of coronavirus emerged in the Auckland community.
Flights incoming to Queensland, NSW and Victoria from New Zealand from 12.01am Monday will be subject to "red zone" rules for at least a period of three days, the officer of Australia's Chief Medical Officer Professor Paul Kelly.
Anyone who arrives after this time from anywhere in New Zealand will be required to undergo 14 days of supervised hotel quarantine.
Professor Kelly convened an emergency meeting Sunday evening to discuss the current snap three-day lockdown underway in New Zealand after three members of the same family tested positive to Covid-19.
The country's health authorities have yet to determine where they acquired the infection.
People who have arrived in the three Australian states already will be dealt with by their respective states.
"States will determine how to manage people who have already arrived in Australia from New Zealand and who may pose a risk of transmitting the Covid-19 virus," a statement from the CMO's office said.
"The National Incident Room will assist states and territories by seeking relevant flight manifests."
Uncertainty surrounding Victoria's lockdown
Health authorities say it is too early to tell if Victoria's snap lockdown has worked as new cases emerge from a family function in Melbourne's north.
The two new cases reported on Sunday were a three-year-old child and a woman in her 50s from separate households who were at the Coburg event on February 6.
The function was attended by 38 people including a worker at the Holiday Inn quarantine hotel at Melbourne Airport, bringing the total number of cases linked to the outbreak to 16.
Health Minister Martin Foley would not be drawn when asked if Victorians could be confident the "circuit breaker" lockdown would not be extended beyond Wednesday.
"It is too early to say whether we have been successful," he told reporters on Sunday.
"But the signs show Victorians are doing the right thing, backing each other, and our test, trace and isolate system is staying ahead of this.
"We will continue to monitor it on a day-by-day basis, really it is up to the shared effort of all Victorians."
Despite the reassuring rate of negative results from Saturday's tally of 21,475 tests, Chief Health Officer Brett Sutton rejected a suggestion the five-day lockdown was an overreaction.
"This is a high stakes game," Professor Sutton said.
"We cannot afford to be wrong here."
It came as authorities were forced to defend the time taken to identify the venue at 426 Sydney Road, Coburg as an exposure site.
Victoria's COVID-19 testing boss Jeroen Weimar said the Holiday Inn worker, her partner and housemate as well as the three-year-old child and woman in her 50s were among 38 people who attended the event.
The worker had returned a negative test result the following day but a subsequent review found it was a "false negative".
"To be a weak positive, but to be infectious enough to actually cause infection in other people at an event is very unusual," Prof Sutton said.
The child's mother could be another possible case in waiting after returning three conflicting test results in a 24-hour span.
Officials are yet to determine whether she is at the start or tail end of her infection, Mr Weimar said.
Do you have a story tip? Email: email@example.com.