Prime Minister Jacinda Ardern has admitted the COVID-19 outbreak "obviously hasn't come from within New Zealand" after the Director-General of Health said it must have come through the border.
But the Prime Minister said there is still no evidence to suggest the latest outbreak came from the Government's managed isolation and quarantine (MIQ) facilities or that it was passed on through border workers.
The Director-General Ashley Bloomfield told The AM Show on Tuesday officials are confident the virus "hadn't laid dormant" in the community and said it "must have been introduced through the borders" either at the airport, MIQ or one of the ports.
Ardern, appearing later on the show, said there was "still no evidence" of that from research by ESR, New Zealand's Crown Research Institute, which has been performing genome sequencing on positive coronavirus samples.
"We did a sweep of testing across all those frontline border workforces, across the port, across all our managed isolation facilities. You'll know that we also genomed everyone that was in our MIQ to try and find matches there. We did not find the source," Ardern told The AM Show.
But when asked later in the day if Dr Bloomfield was wrong to say the outbreak came from the border, Ardern said both she and the Director-General's responses were correct.
"In that case we both can be. We haven't been able to demonstrate through evidence of all the testing we've done where it's come from, but ultimately it obviously hasn't come from within New Zealand," Ardern said.
"We know that from the work that ESR has done from the type that we have and we know that from the amount of time and the amount of mutation. We know it's come in from somewhere, so technically it has to have come from outside.
"What of course we haven't been able to prove is that it's come in from our MIQ or through border workers; that we haven't been able to demonstrate."
Ardern has fiercely defended claims by National Party leader Judith Collins that the COVID-19 outbreak in Auckland was caused by a "border mishap".
Collins has suggested the virus outbreak is linked to the border after Newshub revealed more than 60 percent of border-facing workers had not been tested the week before the latest outbreak, falling short of Cabinet's approved testing strategy.
The Government has since ordered all border-facing staff to be tested.
The south Auckland cluster is understood to have originated at cold storage facility Americold in Auckland but the source is still unknown, and Ardern said last month there are a "number of ways" the virus could have entered New Zealand.
"To date we have not established the source of the cluster but we are working hard to investigate all possible options," she said, although Dr Bloomfield has all but ruled out transmission from cold store goods.
The minister in charge of MIQ, Megan Woods, said earlier this month she had been advised that it was unlikely Auckland's COVID-19 outbreak came from the state-run facilities.
Dr Woods said one of the "first pieces of work we did" after the outbreak in Auckland was to try and match it up to the positive cases of COVID-19 in MIQ facilities.
"None really fitted with the timeframes when we think the most likely first entry point would've been to fit with that community cluster," she said.
The Ministry of Health reported three new cases of COVID-19 in New Zealand on Tuesday, all detected in recent returnees in MIQ facilities.
The total number of active cases in New Zealand is 83, including 28 in MIQ facilities and 55 in the community all linked to the Auckland cluster.
The case of a healthcare worker from the Auckland quarantine facility has been genomically linked to the Auckland cluster. The case is most closely linked to three cases from the cluster who were staying in isolation at the facility.
Officials are continuing to investigate how the infection occurred.