Three Aucklanders died of the flu this year, including two children. The deaths included a 4-year-old boy, a 12-year-old girl and a 77-year-old woman.
Two others are believed to have died in Wellington and Christchurch.
The girl - who had existing health problems - died in September, and was the last person to fall victim to the flu in the Auckland region.
"Because of her underlying condition, it probably pushed the flu to the worst possible outcome," said Dr Sue Huang, principal investigator for the Shivers Project, a five-year influenza monitoring programme in the Auckland region.
Last year, four Aucklanders died of the flu.
Data from the Ministry of Health is not yet available for influenza deaths for the past two years but there have been at least two more deaths this year - one each in Wellington and Christchurch.
Huang said there were probably around 400 more deaths a year which involved influenza as a contributing factor, but could not be considered the primary cause of death.
According to the Shivers Project, the number of flu cases in Auckland was slightly down
There were 31.9 hospitalisations per 100,000 population and 17 admissions to intensive care, down from 40.6 and 25 respectively last year.
Huang said this year there was a resurgence in H3N2 Influenza, the predominant strain early in the season. Influenza B became the most common in late winter.
Last year, H1N1 was the leading cause of illness, but that declined to almost single digits this year, Huang said.
New Zealand and Australian health officials have updated the vaccines to be used next year.