The National Influenza Centre says the deaths of a child and an elderly woman this flu season could be the tip of the iceberg.
The centre said a four-year-old boy and a 77-year-old woman died after catching the infection, but the real number of deaths could be much higher.
Last week there were five times as many cases of influenza across the country than at the same time last year.
The Government has extended the free vaccine programme until 11 September.
The centre's director, Sue Huang, said both deaths were in Auckland, but data for the rest of the country would not be available for up to three years.
She said influenza could often be a trigger for other health problems, such as cardiovascular disease, which could mean patients were hospitalised.
But it may not have been identified as being behind the complications which ultimately led to the patients' deaths.
"So they went to hospital, they died. Eventually their diagnosis is cardiovascular disease or some other disease ... but actually the trigger can be influenza."
Ms Huang said it was difficult to assess that figure.