The racing industry has been vocal in its support for an ongoing vaccination programme against the disease, believing is will help the industry recover more quickly in the event of future outbreaks.
The industry has been lobbying the federal government to allow an ongoing programme.
However, vaccination is opposed by many industry groups, including the Australian Veterinary Association (AVA) and the Australian Horse Industry Council (AHIC).
"As equine influenza has now been eradicated from Australia, the debate will be around whether horses should continue to be vaccinated to protect them against possible future outbreaks," says Dr Jane Axon, president of Equine Veterinarians Australia, a special interest group of the AVA.
"There are vocal groups calling for continuing vaccination, but this is not the answer.
"The AVA does not support ongoing vaccination as this will not stop another outbreak. Only strong and effective quarantine systems can keep this disease out of this country.
"The horses that brought the disease into Australia last year were all vaccinated. The problem is, because equine influenza has the capacity to mutate, even vaccinated horses can catch a new strain of the virus.
"Vaccinating the horses against equine influenza is only protecting against a disease that exists today. Unfortunately the virus can mutate and have a completely different shape tomorrow, and a vaccinated horse can catch it," Dr Axon says.
"Vaccination simply masks the symptoms of equine influenza and makes it even more difficult to spot. By the time the signs of the disease are visible you could have a huge outbreak and suffer the same devastating effects which the equine industry is still getting over.
"The most crucial thing we can have to protect horses in this country is a strong, science-based quarantine system that works effectively."
The racing industry has said it is prepared to pay the cost of ongoing vaccination of its horses. It has enlisted at least two experts who believe ongoing flu vaccination is the appropriate course.
Dr James Gilkerson, an equine virologist at The University of Melbourne's equine infectious disease laboratory, voiced his opposition to ongoing vaccination in June.
"Only an effective quarantine programme will prevent another outbreak. Ongoing vaccinations won't help," he said.
"Instead of ongoing vaccination, Australia needs to maintain emergency registration of a range of vaccines for use in case there's another outbreak."
The AVA, in an earlier statement, said experiences in other countries backed its position against ongoing vaccination: