It will arrived in the country within a week.
Federal Agriculture Minister Peter McGauran said the Commonwealth, States and Territories had agreed the vaccine would be used in New South Wales, and, if necessary, in Queensland, to reinforce buffer zones around areas where there were large numbers of infected horses.
"The vaccine that will be imported is considered to be the most effective vaccine for combating equine influenza in the emergency situation currently in Australia," McGauran said.
"While the vaccine is a vital part of the containment and eradication strategy, it remains important that all horse owners continue to comply with standstill provisions where they apply, maintain good biosecurity practices, and report suspect cases of the disease as early as possible.
"Vaccination, in isolation, will not provide a quick fix for eradicating equine influenza.
"The vaccine has been approved for emergency use in Australia by the Office of the Gene Technology Regulator and the Parliamentary Secretary to the Minister for Health and Ageing, Senator Brett Mason.
"This live vaccine, ProteqFlu TE, from the Merial Laboratory in France, will only be used for disease control in nominated buffer zones. It has not been approved for any other purpose."
Mr McGauran said that using the vaccine for emergency purposes was consistent with the Australian Veterinary Emergency Plan and, initially, up to 5000 horses may be vaccinated in buffer zones in NSW to assist with disease containment efforts.
"Strict movement controls will remain in place around all infected areas to make sure horses do not leave these areas," he said.
"Buffer zones will be established around infected areas and some horses may be removed from these areas as an added control measure," Mr McGauran concluded.
Although use of the vaccine will be targeted, the National Equine Influenza management group is said to be drawing up a contingency plan for mass horse vaccinations if the flu outbreak cannot be contained.
However, a national vaccination programme would be expensive, with the need for boosters and ongoing changes to the vaccine to combat new strains. Authorities consider containment and eradication remain the best strategies.
Meanwhile, authorities in Western Australia confirmed that 19 international horses on a plane at Perth Airport had been approved by the Australian Director of Quarantine and would pose no threat of introducing equine flu.
"Eighteen of the horses were from New Zealand, which was free of Equine Influenza," said WA's Agriculture and Food Minister Kim Chance.
The remaining horse, imported from the United States, travelled with the New Zealand consignment to Perth after an extended quarantine period at the Spotswood Quarantine Station in Victoria.
"These horses pose no risk to WA's Equine Influenza-free status," Mr Chance said.
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