A "weak positive" case has tested negative this morning, meaning there are no new cases of Covid-19 to report today.
Director general of health Ashley Bloomfield said the person likely had a historical infection.
They had been on the same chartered flight from Christchurch to Auckland 11 days ago as the man whose Covid-19 is thought to have had a long incubation period.
But the person is thought to have had Covid-19 before they came to New Zealand. They tested negative twice while in managed isolation and have had no symptoms since arriving from India.
"This person remains under investigation to confirm that this is an historic case, and whether it has already reported as a case in India," Bloomfield said.
In the meantime, the person has been transferred to the Jet Park Hotel as a precaution.
The person's gathered RNA was being looked at to see if it matched any other genome sequencing, he said.
All other 28 people who were in the first nine rows of the chartered flight have tested negative.
Bloomfield asked people to remain vigilant as they moved into lower alert levels.
"The risk of Covid-19, although small, does remain."
There are now 39 people isolating in the Jet Park quarantine facility from the community, which includes 18 people who have tested positive and their household contacts.
Three people are in hospital with Covid-19 – one each at Auckland City, Middlemore and North Shore hospitals. All three patients are in isolation on a general ward.
There are 4003 identified close contacts in the Auckland cluster, of which 3992 have been contacted.
The total number of active cases is 61 - of those, 29 are imported cases in MIQ facilities, and 32 are community cases.
There were 3278 tests conducted yesterday, and Bloomfield said there tended to be fewer tests at the weekend.
Yesterday, Cabinet decided to move Auckland into full alert level 2, with a 100-person limit on social gatherings, from 11.59pm tomorrow, September 23.
The city will remain at level 2 for at least two weeks.
The rest of the country moved to level 1 this morning.
Aucklanders are being asked to take level 2 restrictions with them if they leave Auckland.
How to deal with positive tests for historical Covid infections
Bloomfield said test results came through from time to time that were historical cases of Covid-19.
These were weak positives and research showed they were not infectious.
"Over the past two months we have seen four different examples of this," Bloomfield said.
There are those who returned a positive test after leaving New Zealand and arriving in another country, but who were not recently infectious before leaving New Zealand.
There are those who arrived in New Zealand and tested positive in managed isolation – or subsequent to leaving managed isolation – without acute symptoms.
There are those who tested positive who had already recorded an infection and are already in New Zealand's case count.
And there are those who tested positive and have not already recorded an infection, but who have clear history of a previous acute illness consistent with Covid-19 and were not tested at the time. Follow-up serology testing confirms that they (and possibly other members of their family) have been infected in the past.
Bloomfield said a panel was now setting up a protocol to manage such cases.
Testing people coming into contact with Aucklanders
Testing would continue to focus on people with symptoms, but also those who come into contact with Aucklanders travelling around the country including tourism and hospitality workers.
That would include people who didn't have symptoms, Bloomfield said.
The DHBs are making mobile testing sites available, and they could be set up at airports, he said.
Should we keep wearing masks at alert level 1?
Bloomfield said wearing masks was of most value where there was community spread, and people at level 1 were still encouraged to use them on public transport, which he would continue to do.
Cabinet ultimately decided to leave level 1 as it is, which is essentially life as normal but with border controls and for people to be vigilant about washing their hands, getting tested if sick, and keeping tabs on their movements and who they're with.
Otago University epidemiologist Professor Michael Baker said the Government has "missed an opportunity" to have ongoing mask use on "high-risk indoor activities" - like clubs, concerts and large gym classes - and on public transport and planes.
Baker said that should continue until there was total confidence the virus had again been eliminated - which is when there hasn't been community transmission for 28 days.
Bloomfield said he advised Cabinet to consider a 500-person limit for indoor gatherings outside Auckland, and Cabinet had decided instead to look at identifying such gatherings and providing health advice.
He hadn't recommend a 500-person limit to Cabinet, he added.
He said yachts off New Zealand could drop anchor here if they were in distress, which would be decided on a case by case basis. Many of them can sail on and avoid cyclone season, he added.
"There is nothing preventing them before cyclone season from sailing back to their home country."