Masks will be mandatory for everyone travelling on domestic flights and for Aucklanders using public transport as early as Thursday.

Until then, New Zealanders are being urged to act like face coverings are already compulsory despite the mystery lifting about the source of the latest community Covid-19 case.

After just over 24 hours, Auckland's CBD was yesterday shifted out of its quasi-lockdown after genomic testing proved the AUT student was infected by the Defence Force serviceman from the quarantine cluster. The chain of transmission is still being investigated.

The genomes from Case A - the serviceman who caught the virus in the Jetpark quarantine facility - and Case D - the AUT student - were identical, which is consistent with direct transmission between the two.

That doesn't exclude the possibility of someone else being in the chain, but officials are confident the time-frame suggests there was not a long chain of transmission involving a lot of people.

There were no other positive cases of Covid-19 in the community yesterday despite more than 7200 tests being processed, including more than 100 from the woman's Vincent Residences apartment building.

As a precaution, everyone who visited one of the locations of interest is being asked to get a test regardless of whether they have symptoms.

But how the AUT student was infected is still a missing piece of the puzzle.

The woman works just 82m from a cafe the defence worker visited, but extensive interviews haven't uncovered an obvious connection.

Among the avenues being investigated is a public toilet, but initial reports suggest that is not the missing link.

Despite confidence the cluster is well-contained and widespread transmission is highly unlikely, Covid-19 Response Minister Chris Hipkins will move next week to make masks mandatory on planes and on public transport in Auckland.

The public health order is being drafted and will be presented to Cabinet on Monday with the support of the Prime Minister.

Once agreed and gazetted, it will take 48 hours to come into effect, which means it could be in place by Thursday morning.

Mask use will initially be mandated on all domestic flights and public transport in Auckland, but it's likely other areas which have MIQ facilities or international airports will be included in the order later.

The order is similar to the one issued in August requiring mask use under alert level 2; children and those with medical conditions will be exempt.

It's understood the Government will encourage a light-handed approach to enforcement with a focus on educating rule-breakers before issuing the instant $300 fine.

Hipkins was questioned yesterday about why it took a near-crisis for the Government to heed the advice of expert epidemiologists who have long been calling for mass-masking.

He replied that advice was continuously being reviewed.

Infectious diseases expert Professor Michael Baker welcomed the move but said he was surprised it took so long to be brought in.

"We're probably one of the last countries in the world to adopt mass masking, so it is a bit out of step with the other aspects of our response which have otherwise been world-leading."

Baker also wants a wider review of the alert levels which haven't been adjusted since March and would like to see an alert level 1.5 with mass masking which would heighten awareness but still have society functioning.

"The current system really is far too crude."

Hipkins announced yesterday he was considering requiring some events and venues to make it mandatory for patrons to sign in upon entry. Those are likely to be large gatherings and hospitality venues where physical distancing isn't possible.

In the interim he has urged businesses to ensure QR codes are visible and encourage their customers to scan in and has asked New Zealanders to be vigilant with scanning QR codes in the Covid Tracer app.

"It helps enormously with the speeding up of contact tracing and helps us get ahead of the virus."

Data from the Ministry of Health showed fewer than one in six of the 2.3 million users of the app use it daily.

And it was revealed there was another breakdown in communication between the minister and health workers on the ground.

Hipkins said he'd expected public health protection officers would be at the Vincent Residences, where the AUT student lives, on Thursday evening but it became apparent yesterday morning that hadn't happened.

Numerous media outlets reported people were seen leaving the apartment block despite being asked to stay put.

Hipkins said the risk for the apartments was "relatively low" and no one had yet returned a positive result, but it "would have been nice" security had been there "right the way through".

"As soon as I became aware of that I got on the phone and made sure that happened."

New Zealanders are also being asked to put themselves in the shoes of the four people at the centre of this outbreak who "understandably feel the weight of the entire country on their shoulders".

"Being in the eye of the storm" could have an impact on their ability to recall their movements and interactions, which could hamper the speed of contact tracing, he said.

"It is the virus that's the problem and not the people. They do not deserve to have blame heaped upon them. They need our support."

He also thanked border workers, who are some of the most scrutinised and tested people in the country.

"While they might not feel it all of the time, we are truly grateful for the sacrifices they are making, for their professionalism and for their compassion."

Locations of interest

• Mezze Bar on November 5.
  • Liquor.Com bottle store, Queen St, on November 5.
  • Red Pig Restaurant on November 7.
  • Smith and Caughey's Queen Street on November 7.
  • Sunny Town China Taste Restaurant on November 8 and 9.
  • Starbucks Queen Street on November 8 and 9.
  • The Gateau House on November 8.
  • A-Z Collection on November 8, 9, 11.
  • The Vincent, November 7-12.
  • Auckland City Doctors on November 10.
  • AUT Student Hub on November 10.