The National Influenza Centre says research for flu vaccines cannot keep up with the speed at which new strands of the virus develop.
Health officials around the world have been discussing the likely make-up of next year's influenza virus as they try to develop an effective flu shot.
It follows a winter where 8 percent of people who got the flu are believed to have contracted a rogue strain of the virus not covered by the flu shot.
The World Health Organisation (WHO) makes recommendations at this time each year to give national public health authorities a guide for the development and production of flu vaccines for the following year.
However, it takes at least six months to produce the vaccines - by which time a new strain might have emerged.
In New Zealand, the National Influenza Centre said most sufferers this year had the H1N1 strain, but director Sue Huang said some vaccinated people still caught a new strand, H3N2, which the shot did not protect against.
"It's like you are trying to predict the weather, you predict six months in advance, you choose a strain, and six months down the line, the virus has already mutated," she said.
A clinical virologist to the Canterbury District Health Board says while flu shots are not 100 percent effective, they are still the best way to protect against the illness.
Lance Jennings said the number of people getting the H3N2 virus seems to be increasing and older people are more susceptible.
Mr Jennings said the vaccine is not as good as they would like, but it is extremely effective in reducing the severity of the illness and preventing pneumonia.