Four cases of the Omicron subvariant BA.5 and one case of BA.4 have been detected in the community with no clear link to the border for the first time.
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Meanwhile, another 14 people with Covid-19 have died and 6232 new cases have been identified in the community, the Ministry of Health said.
There are 390 people in hospital, down slightly from 393 yesterday, with eight in ICU.
The Ministry said the variants' presence in the community is not unexpected and further cases are expected.
"These Omicron subvariants are prevalent overseas and have been detected at our border for many weeks."
It also reported seven cases of BA.2.12.1 in the community.
"Emerging data suggests BA.2.12.1 is marginally more transmissible than BA.2, the dominant subvariant currently circulating in Aotearoa-New Zealand. There is some clinical data to suggest the BA.5 and BA.4 subvariants have increased transmissibility when compare to BA.2, but no data suggesting they cause more severe illness.
"The vast majority of recently sequenced cases in New Zealand continue to be of the Omicron BA.2 sub-variant, with small number of cases with the BA.1 sub-variant."
BA.4 or BA.5 has been detected in Auckland, New Plymouth and Porirua wasterwater and BA.2.12.1 in Auckland, Bay of Plenty, Palmerston North and Taupō.
"Together the community cases and wastewater results suggest that the BA.4/5 and BA.2.12.1 Omicron subvariants are circulating in parts of the community in New Zealand."
Deaths and cases
The 14 deaths reported today include the historical death of a case late in 2020. The ministry said this case had recovered at the time of death but was recently classified as having Covid-19 as a contributory cause of their death.
"This will continue to happen occasionally due to the timing of the mortality coding process, particularly in instances where deaths where Covid-19 is a contributory cause, and the death falls outside of the 28 day period of testing positive for Covid."
Today's deaths include two people in their 60s; three in their 70s; three in their 80s and six aged over 90. Four were women and 10 were men.
One was from Northland; three were from the Auckland region, one was from Taranaki; one from Whanganui; one from the Wellington region; one from Nelson-Marlborough; four from Canterbury; one from South Canterbury and one from the Southern DHB.
The total number of deaths in New Zealand of people with Covid-19 has risen above the 1200 mark, with 1210 deaths.
The seven-day rolling average of community case numbers today is 6850, down slightly from last week's 6960.
Today's cases were reported in the Northland (161), Auckland (1907), Waikato (443), Bay of Plenty (196), Lakes (77), Hawke's Bay (189), MidCentral (227), Whanganui (73), Taranaki (177), Tairāwhiti (45), Wairarapa (55), Capital and Coast (556), Hutt Valley (237), Nelson Marlborough (239), Canterbury (1007), South Canterbury (99), Southern (467) and West Coast (73) DHBs.
There were also 69 cases reported at the border.
Yesterday there were 13 deaths of people with Covid-19 reported and 7870 community cases.
There have now been 1,179,634 cases of Covid-19 reported in New Zealand.
Covid-19 modeller Michael Plank has warned that a second Omicron wave, likely in the next three to four months, could result in higher numbers of hospitalisations and deaths.