NB.1.8.1 is now the dominant strain in China and Hong Kong. ABC News reports it is also driving up infections in Australia.
Here, the latest available ESR wastewater testing to May 11 shows the sub-variant making up 21.6 percent of readings.
Epidemiologist Michael Baker said it came as overall Covid-19 detections were surging.
"We've had a long period when Covid levels have been relatively low in New Zealand. It's about 11 months since our last big wave, the sixth wave, in June last year."
Baker said there were numerous surveillance systems giving an idea of how the virus was spreading, and most were not showing changes. However, that was not the case for wastewater testing.
"There's quite a striking spike in the wastewater samples and the positivity detected there. And numbers are really shooting up across the country, so for the first time in around 11 months we're seeing what looks like the beginning of a wave."
Baker cautioned it was too early to see a clear picture, and further results over the next week or two would help.
"But I think it is a strong warning that we should be taking more action around Covid-19 in various ways."
Baker said NB.1.8.1 was becoming dominant in a number of countries and it would "almost certainly" do the same in New Zealand.
"We see many new subvariants and most of the time they're not translating at the moment into a rise in cases.
"But that's why this one is different - we are seeing that early increase, but we're not seeing it in all the surveillance systems yet, so we just need to keep watching.
"I think the message is very clear that we're moving into winter, we have got this rise in cases - and if anyone has been putting off getting their Covid-19 booster, now would be a good time to get it."
Baker said health authorities should also be taking additional precautions in hospitals, residential care facilities in particular.
He said the existing vaccine gave added protection against the new subvariant, which descended from a variant the vaccine is based on.
"I think it's all adding up to a picture of the need to take precautions against this infection."
