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As Auckland wakes up united in alert level 1 with the rest of New Zealand, a leading epidemiologist is calling for a total overhaul of the border operation.

Nick Wilson, a professor at the University of Otago, wants the Government to build purpose-built facilities in military bases away from city centres to prevent further incursions.

He called the current border response "highly problematic", which was putting the nation at risk.

"The failure rate is just so unsustainably high, with now 11 border failures since last August."

He even suggested the Government halt all returnees except for those with legitimate humanitarian needs "so we have time to get our act together at the border".

He said at the very least the "tap should be turned down" until the border system could be reviewed and its safety assured.

Covid-19 Response Minister Chris Hipkins today said there was enough vaccine for a second booster jab to be given to all border workers and their families.

He told Newstalk ZB's Mike Hosking MedSafe was working through the approvals process for the three other vaccines expected to be administered to the remainder of the population later in the year.

At this stage the timetable still remained for this to happen in the second half of the year.

A second shipment of the Pfizer vaccine was expected in the near future, with further smaller batches arriving regularly over the next couple of weeks, Hipkins said.

Hipkins said the remaining vaccines would gain Medsafe approval before any deliveries.

He said when the larger rollout happened later in the year people would not get a choice of vaccine.

"Ultimately it will mostly be determined by logistics," he said.

Hipkins said it would depend on the efficacy of the vaccine to achieve herd immunity and its success in reducing transmission that will determine whether border restrictions were eventually relaxed.

Wilson's calls came just before Auckland moved back to alert level 1 at midnight, after a week of restrictions to contain and trace the Valentine's Day cluster.

Another family member of the previously confirmed cases tested positive yesterday but they were already in quarantine as a precaution so the case was deemed "very low" risk.

Eight people have tested positive from the outbreak, which is considered well-contained even though the source of the transmission is still a mystery.

Cabinet also decided to continue mandating mask use on public transport and for Uber and taxi drivers across New Zealand, with exemptions for food services on flights and for children under 12. The move was celebrated by scientists who have long called for the rule.

An aerosol chemist at the University of Auckland, Joel Rindelaub, said public transport could be a high-risk environment because of limited ability to socially distance and said "it is a wise move to take a cautious approach".

Prime Minister Jacinda Ardern said she hoped face coverings would "become a part of normal life".

The order will continue to be reviewed as the vaccination programme - which started with border workers at the weekend - is rolled out through the general population from the middle of the year.

Ardern poured cold water over the need for purpose-built quarantine facilities.

In the year it would take to get New Zealand's "team of five million" immunised, evidence could emerge that vaccination reduced transmissibility, Ardern said.

And that could "change up" what was required at the border.

In the meantime, constructing a purpose-built facility which could hold up to 6000 people was a "significant ask", especially as some incursions were traced to returnees touching the same lift button, Ardern said.

"So not always has the facility been the problem, but the virus within it."

More than 113,730 people have moved through the managed isolation system with 11 outbreaks in the community in that time.

But Wilson called it "crazy" to have the managed isolation facilities in Auckland and wants purpose-built facilities in military bases where factors such as ventilation could be controlled. His call was supported by the National Party at the weekend.

He pointed to ventilation at the Pullman Hotel shifting from two hours a day to 24 hours after recent returnees later tested positive after leaving the facility.

"What's it like at the other hotels? I think the whole thing is highly problematic and we're risking the health of the team of five million."

Wilson is set to meet the Ministry of Business, Innovation and Employment tomorrow and Covid-19 Response Minister Chris Hipkins on Thursday and will raise his concerns.

Hipkins has previously pushed back against Wilson and fellow expert Michael Baker calling the outbreaks "border failures" because he said it affected the morale of workers.

"My request is, really, let's be a bit supportive of our border workers. Let's not label their efforts as failures or their successes as 'down to good luck'. It's actually down to hard work," Hipkins said last Wednesday.

Wilson said the Government refusing to call the outbreaks "border failures" was a "very clever communications skill".

"It's just so clever, these deflections, because people will believe it. People like to blame people - they don't think about blaming the system when it's almost always a system problem. And it's just human nature to blame someone."