The second Whatawhata case is an older case which was previously reported as Hamilton, but had been moved over.
It comes after director general of health Dr Ashley Bloomfield announced a total of 94 cases; the remainder of which are all in Auckland.
The 94 cases represents the biggest number of daily cases in New Zealand since the outbreak started in March 2020.
Previously, there had been two days of 89 cases each, in early April 2020.
Prime Minister Jacinda Ardern said vaccines were making a significant difference to the outbreak and that today's cases were a result of "non compliance" of alert level 3 restrictions.
Meanwhile, in Te Awamutu and Whatawhata, residents with symptoms are now being urged to get tested.
Common symptoms of Covid-19 include a fever, cough, tiredness and a runny nose.
Other symptoms could include a headache, aches and pains, diarrhoea or a skin rash.
Pop-up testing stations had been set up this morning but had either closed - or will close soon.
One outside the Te Awamutu Events Centre will close at 3pm while a site at Kihikihi Domain closed at 2pm.
A Waikato DHB spokesman said the Whatawhata testing site was announced yesterday as public health were investigating information that a case had spent time in the area, although no locations of interest have been identified at this time.
A total of 66 per cent of Hamilton City residents were now fully vaccinated, just behind those in Waipa on 67.3. There were 61.8 per cent in the Waikato district.
Overall in the Waikato region, it had an average of 62.6 of residents fully vaccinated.
Waipā deputy mayor Liz Stolwyk urged people to get tested if they had symptoms, and isolate at home until the result is received.
"We need to ensure anyone who needs it, gets tested. Even if you have just a runny nose, get tested. It is imperative we stamp out Covid-19 in our community."
No locations of interest have been released, but Stolwyk asked for residents to keep an eye on the list on www.health.govt.nz in coming days.
There was also a pop-up testing station opened at Te Papa o Rotu Marae in Whatawhata until 3pm.
Waikato District councillor Noel Smith said it had become apparent that people were either apprehensive or for some other reason not getting tested when they had symptoms.
"It is absolutely imperative in the interest of whanau, wider family, friends that people get tested then we can as a community support those people recover and protect the remainder of our vulnerable community."
Residents expressed their concern on social media about the possible cases. There were also reports of people in the town self-isolating.
Smith said a lot of people had questioned why district borders were being used instead of sub-regional borders.
"But of course now it is looking like there was a case in Whatawhata, it brings it closer to home," he said prior to the 1pm announcement.
