Chair of the Environmental Risk Management Authority's decision-making committee Dr Kieran Elborough says the vaccines can only be used if there is an outbreak of equine influenza in New Zealand or to meet the biosecurity requirements of other countries for horse imports.
The committee considered that the potential benefits of the vaccines ProteqFlu and ProteqFlu Te outweighed the risks.
The two vaccines have the same GM component, but the latter provides additional protection against tetanus.
The vaccines have been approved by the European Medicines Agency since 2003.
The application was submitted by the New Zealand Racing Board and the New Zealand Equine Health Association.

Omakau harness racing day.
Conditions placed on the use of the vaccine include that it can be administered only by a trained veterinarian and records of the vaccine use must be maintained and made available to the Ministry of Agriculture and Forestry Biosecurity New Zealand.
The vaccines must be stored in a secure location and expired vaccines must be disposed of as hazardous waste.
The full decision document can be found on the ERMA New Zealand website.