Ian Macdonald was quoted in the Sydney Morning Herald newspaper in support of Racing NSW's bid to have national compulsory vaccination of thoroughbreds and other competition horses as part of a "risk management" plan.
The minister was reported as saying: "You would vaccinate twice annually your performance horses and it wouldn't be compulsory for all other horse breeders. It would be optional."
He referred to resistance from other states, saying: "Most of the world does vaccinate ... There is a massive risk of not vaccinating."
The Horse Industry Council said the minister's comments were concerning.
"There is to be a national summit in Sydney on September 25 to discuss future options for equine influenza management in Australia," the council said.
"The minister's comments - if accurate - seem premature, given that the summit has not yet taken place.
"AHIC surveys and other feedback clearly indicate that the majority of participants in the Australian horse industry, including the racing sector, do not favour ongoing vaccination against equine influenza."
Several groups have spoken against ongoing vaccination, including the Australian Veterinary Association.
It has urged the Australian government to ignore calls from thoroughbred and racing organisations for the continuation of the EI vaccination programme.
"Only an effective quarantine programme will prevent another outbreak. Ongoing vaccinations won't help," said Dr James Gilkerson, president of Equine Veterinarians Australia, a special interest group within the association.
He said in June: "Ongoing vaccination won't prevent another outbreak – the horses who brought the disease with them last year were all vaccinated. Vaccinated horses can still get equine influenza and spread it to unvaccinated horses.
"Also, if there's another outbreak, there's no guarantee that the vaccination being used will work if there's a new strain of the virus. Flu viruses mutate regularly, and imported horses could easily bring in a new strain. We would be vaccinating with yesterday's vaccine against tomorrow's virus.
"Effective quarantine is the only way of preventing another costly outbreak."
Meanwhile, Australian horse breeders expect to receive legal advice shortly on whether they have a case for compensation over the EI outbreak, which began a year ago this week.
Breeders estimate they lost about $A1 billion over the outbreak.