The Government is working on the basis that the Covid-infected Sydney who visited Wellington has the more-infectious and deadly Delta variant.
Covid-19 Response Minister Chris Hipkins' comments come as the Government awaits results of genome sequencing from Australian health officials, which were expected last night.
"From past experience the time to do genome sequencing can vary, depends on the strength sample."
Hipkins had been assured as soon as Australian authorities had the results, they would share it immediately.
He expected this to occur this evening but already they were assuming it was the Delta variant.
"We are working on the basis it is likely to be the Delta variant. The advice from Australia is that it is linked to their outbreak [in Sydney] at the moment, which is the Delta variant."
Earlier today Hipkins said there were no new cases of Covid-19 in the community or in MIQ to report.
However, he cautioned "it's still early days".
There were around 7000 tests processed, over 1200 in Wellington region - four times more than usual.
Hipkins said the Government is still waiting for the genomic sequencing results from Australia after a Sydney man travelled to Wellington on the weekend while infected with Covid-19.
Hipkins said there had been good, fast and efficient flow of information in both directions between Australia and New Zealand.
The man's partner, who he travelled with, is asymptomatic and tested negative for the virus.
It comes amid fears the virus could be anywhere in New Zealand, due to the high transmission rate of the variant and fact many people moved in and out of Wellington over the weekend.
Wellington moved into alert level 2 at 6pm yesterday.
Hipkins said this was not a lockdown. The measures at alert level 2 were in place to allow contact tracing.
The number of close and casual contacts is expected to increase as that effort continued.
The results of that would help with Cabinet's review of the situation on Sunday morning.
No further decisions unless there was a need to escalate would come until Sunday.
New Zealand would be looking at including other states in the quarantine-free travel pause if travel continued with NSW, Hipkins said.
The epidemiological link has been confirmed to the cluster in Sydney, Director-General of Health Ashley Bloomfield said. The variant would be known this afternoon.
Regardless of the variant the response remained the same.
The traveller had one vaccine dose about 10 days ago. His partner had one dose also.
Wastewater testing for Wellington was taking place and results would be known tomorrow.
"As learned from Auckland experience the people who need to be tested are the ones who should be tested," Bloomfield said.
There were 420 contacts attached to the contact tracing database who were in locations of interest at the same time as the Sydney man, including 58 who were on the flight to New Zealand. All those on the flight were close contacts.
People were being asked to isolate for 14 days for a reason, regardless of if they returned a negative day five test, Hipkins said.
Bloomfield said colleagues in Sydney said the Sydney man was being "very helpful". They had been using the app. About 60 people received a push notification yesterday as a result.
Jack Hacketts and 4 Kings Bar shared the same QR code. Both were considered to be locations of interest.
Bloomfield said it was good those bars had a QR code and good people using it. The more specific the QR code though the better.
Yesterday was also the fourth-biggest day for calls to Healthline, Hipkins said.
There was expected to be further high demand for testing with additional testing centres set up.
"High demand for testing is a good thing," Hipkins said.
If people could not get a test today they were advised to stay home and isolate, Hipkins said.
There was a S70 notice in place, placing a legal requirement on people who were in those places to follow instructions.
Asked about the situation in Fiji, Bloomfield said they were in daily contact with counterparts there. It would be a challenge for them to re-eliminate Covid-19. The key effort would be a strong vaccination campaign in Fiji, which New Zealand was assisting with.
That was a decision for the Cook Islands government, Hipkins said.
The Cook Islands bubble remained open. There were a few people this morning who were asked to be taken off a flight there this morning given information that was provided.
Vaccine stocks running low
Some Māori health providers have been told to slow down their vaccination processes.
"Unfortunately we can't just produce more vaccines," Hipkins said.
The stock levels for vaccines will get down to pretty much zero before big supplies came in next month, Hipkins said.
"There will be a few sleepless nights around that time."