Megan Woods has been advised that it is unlikely Auckland's COVID-19 outbreak came from the state-run managed isolation and quarantine (MIQ) facilities.
Dr Woods, the minister in charge of MIQ, said based on COVID-19 genomic sequencing - the science behind studying different strains of the virus - she has been advised it is unlikely the latest outbreak came from the facilities.
"That's the advice that we're having, yes," Dr Woods said on Tuesday.
The MIQ facilities are where returnees to New Zealand are sent when they arrive back in the country. Day three tests are not compulsory but if you refuse a day 12 test you're forced to stay another 14 days in isolation, and so far 15 people have.
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.
"We did it first of all looking at knowing what strain that the community cluster was - which is the B111 strain - and knowing where that is most prevalent in the world, and we know that is most likely to come out of the UK," she said.
"So, the first thing that we did was go and have a look at all of our positive cases that have returned from the UK in that period and made sure that we had done sequencing on all those, and if we hadn't, could go back to those samples and do genomic sequencing on them as well.
"None really fitted with the timeframes when we think the most likely first entry point would've been to fit with that community cluster but we have gone back and done testing where we didn't have it on a number of our positive returnee samples."
Dr Woods said not every sample is possible to do the sequencing from, because while a relatively small amount of viral load is needed to be able to run a test, a larger amount of DNA is required to be able to do the sequencing.
"So, not each and every sample has been able to be completed, but where they have been, we've certainly been going back," Dr Woods said.
She said ESR, New Zealand's Crown Research Institute, has been doing a "wonderful job" in examining the lineage of the sequences and how they might fit together.
The Government has fiercely hit back at suggestions Auckland's cluster came from 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 ramped up security at MIQ facilities and has deployed an additional 500 Defence Force personnel and trialling new contact tracing technology. It followed several returnees breaking out of the facilities.
The source of the outbreak in Auckland is still unknown but Otago University Professor Nick Wilson has written that "we must have had some failure at the border" for COVID-19 to get back into the community.
The first case that sparked the Auckland cluster was a worker at cold storage company Americold, but Director-General of Health Ashley Bloomfield has all but ruled out transmission from cold store goods.
National Party leader Judith Collins told The AM Show last week the Auckland outbreak has "obviously been caused by a border mishap".
But Health Minister Chris Hipkins said in Parliament on Tuesday there is "absolutely no evidence to suggest that COVID-19 has escaped" from an MIQ facility.
Dr Woods said in Parliament there has been no community outbreak within MIQ to date "which shows the way in which we are managing these facilities; treating everyone as if they could have COVID is our strongest line of defence".
The Ministry of Health reported 14 new cases of COVID-19 on Tuesday, nine in MIQ facilities and nine in the community linked to the Auckland cluster.
