Covid-19 was detected in a wastewater sample in Napier on December 15, the ministry said. There are currently no known cases of Covid in the city.
While it could be a recently recovered case returning to the region shedding the virus, the result may also signal undetected cases in the community.
Health officials are urging anyone in the region who has Covid-19 symptoms, no matter how mild, to get tested.
Three passengers on Omicron flight test positive
The ministry said all of the passengers on the same international and domestic flights as NZ's first Omicron case are being treated as close contacts and isolating in a managed isolation facility.
Two other passengers on the international flight have tested positive for Covid-19 and one further passenger's positive result is being investigated as a historical infection.
These three people have been moved to an MIQ facility. Whole genome sequencing has identified one of these infections as the Delta variant.
Whole genome sequencing for the other two is due later today, the ministry said.
All other passengers have returned negative day 0/1 and day 3 tests.
Urgent whole genome sequencing is being carried out on all positive test results in recent returnees to determine if they have the Omicron variant.
"While the arrival of a new variant is concerning, New Zealand is well placed to manage Omicron cases with isolation and testing requirements for all new arrivals, robust infection and prevention control and PPE measures at airports and MIQ facilities, and frequent surveillance testing of staff who have any contact with recent returnees," the ministry said.
Yesterday it was revealed contact tracing was under way to identify passengers on the international flight from Germany that arrived here on December 10 and the chartered internal flight between Auckland and Christchurch.
The infected traveller is fully vaccinated with two doses of the Pfizer vaccine.
Two more cases linked to Taranaki school cluster
Of the 15 new Waikato cases, six are in Hamilton and six in Te Kūiti. The locations of the three remaining cases were still under investigation, the ministry said.
Two of the new cases required hospital-level care.
Pop-up and dedicated Covid testing sites are operating throughout Waikato in Hamilton, Te Kūiti, Ngāruawāhia, Huntly, Taumarunui, Tokoroa, Putāruru and Ōtorohanga.
Today's 10 new Bay of Plenty cases are all in the Tauranga area. Nine are linked to previously reported cases, and one is still being investigated for potential links.
Contacts were being identified.
Of the three new cases in Taranaki, two are linked to the Eltham school cluster and the third is based in New Plymouth.
Public health staff were interviewing the New Plymouth case to determine links to any previously reported cases.
The sole new case in the Lakes District Health Board region was in Rotorua and a contact of a previously reported case.
In Auckland, 2064 people are isolating at home.
Three people who arrived on flights from the United Kingdom, USA and Singapore have also tested positive for Covid-19 on day 0 and 1 routine tests. They are in managed isolation facilities in Christchurch and Auckland.
Vaccination update
The ministry said both Capital and Coast and Auckland district health boards were close to reaching 90 per cent fully vaccinated for their eligible Māori populations.
For Auckland District Health Board, just 1339 of the eligible population needed a second dose to reach the 90 per cent milestone, while in the Capital and Coast District Health Board region, an additional 1480 vaccinations were needed to reach the mark.
Pacific people across 19 of 20 health boards were now 90 per cent partially vaccinated or higher – with Whanganui due to reach this milestone at any moment with just 57 doses to go.
The ministry said Pacific communities in eight district health boards were now fully vaccinated.
"Four of our smaller DHBs are also fast closing in on 90 per cent fully vaccinated – with Wairarapa DHB needing just 157 more doses, South Canterbury 516 doses, MidCentral 778 doses, and Nelson-Marlborough 1,183 doses to hit the milestone."
Yesterday, the Government announced it had reached the 90 per cent double jabbed vaccination rate across New Zealand.
As of Thursday 3,789,662 of 4,209,057 eligible New Zealanders aged 12 and over were fully vaccinated.
The populations in seven district health boards had now reached the mark with more to reach the milestone in coming days, said the ministry.
It comes as new community cases in the current Delta outbreak continue to hover under the 100 mark, with 91 new infections yesterday, including a Taranaki school cluster growing to 16 and 58 people being treated in hospitals across New Zealand.
Despite no active cases in Gisborne, a worrying sixth detection of Covid in wastewater had health authorities urging people in the district who had symptoms no matter how mild to come forward and get tested.
Booster shot advice
Earlier today, director-general of health Dr Ashley Bloomfield said the arrival of Omicron on our shores could lead to a reduction in the recommended time double-jabbed New Zealanders should wait before getting a booster shot.
Bloomfield said evidence from cases overseas showed the third booster jab was important in the fight against Omicron.
He had been given advice in the past couple of days on the time period between getting the second jab and the booster shot.
Currently, there is a six-month period between those two jabs.
He said the advice he has been given in recent days will be up for discussion among Government officials and ministers.
"It may be that a shorter interval will ensure that people do get that booster and increase their protection at the right time in case we get Omicron in the country."
He expected there would be an announcement on bringing the booster shots forward before Christmas, but that was up to ministers to decide.
Bloomfield told Newstalk ZB there had been no further detections of Omicron in those who travelled alongside the infected person on flights to and across New Zealand.
He said all the people on the flight that brought the people to New Zealand and the linking domestic flight to Christchurch were in quarantine and undergoing testing regimes.
"We'll be watching closely to see if there are any other positive tests."