However, the application does not mean a roll-out of the vaccine across the country.
The vaccine programme which has proved crucial in the fight against equine flu in Australia was delayed for a short time while necessary approval was sought from government agencies for its roll-out.
The New Zealand application is intended as a pre-emptive move to reduce any delays in using vaccine should an outbreak occur in this country.
The equine flu vaccine would also need the approval of the New Zealand Food Safety Authority's Agricultural Compounds and Veterinary Medicines Group before it could be used.
MAF BNZ is seeking rapid approval for a vaccine called Flu Avert I.N. It contains a weakened live equine influenza virus which is administered to horses by the nose.
This vaccine stimulates an immune response that is similar to the response that occurs when the horse catches a virulent wild strain of the virus. The vaccine has been used in the United States since 1999 and also in Canada.
ERMA New Zealand's General Manager, New Organisms, Dr Libby Harrison, says the rapid approval process being used in this case means the flu vaccine meets certain low-risk criteria and can be assessed more quickly than usual as long as the required level of information is provided.
"An application like this requires information on the biological characteristics of the organism and the route of administration of the medicine. If the relevant information cannot be provided to show that the vaccine meets the low-risk criteria we can't proceed with a rapid approval."
Dr Harrison says once ERMA New Zealand's Decision-making Committee has the information it needs, it has to consider whether the application meets the criteria for approval, which include assessing any potential adverse effects on public safety and health, valued species, the environment and natural habitats.
"The committee will then decide what sort of controls should be placed on the use, storage and disposal of the vaccine. Finally, in order to approve the vaccine the committee has to determine that, given the controls, the risks it poses are negligible."