Influenza specialists say flu is in Auckland, Wellington and Christchurch and case numbers are on the rise.
The Institute of Environmental Science and Research says its surveillance shows that Auckland has by far the most cases of flu, especially in hospitals, with Wellington and Christchurch also affected.
It says while overall flu activity is still relatively low, the number of confirmed cases has risen.
Canterbury virologist Lance Jennings says flu is on the rise, but about 26,000 fewer people nationally have had the vaccine so far compared to this time last year.
He says the vaccine is the best protection, but there is complacency, particularly among at risk groups under the age of 65, including pregnant women.
The head of the Emergency Department at Auckland City Hospital says flu is putting considerable pressure on the hospital.
Dr Tim Parke said his hospital had been "very busy, teetering on gridlock" but that the situation had settled down after an initial surge.
Influenza experts say the A H3N2 strain is predominant, particularly among older people, with some H1N1 (or swine flu) in younger people.