"Calls to eradicate flying foxes in an attempt to control Hendra virus are ignoring the facts," said association president Dr Barry Smyth.
"They fly and travel long distances, and would be very difficult, if not impossible to eradicate. In trying to kill them they would become very stressed, and that would increase their chances of spreading Hendra virus."
"Instead," said Smyth, "everyone who works with or cares for horses needs to know the risks, and take appropriate measures to protect themselves and their horses from Hendra."
Smyth's comments came on the day Queensland authorities announced the death of the ninth horse from the virus, in what is an alarming season for cases.
"We understand people's anxiety about this virus. Vets who see sick horses every day are really in the firing line of the disease and the number and range of cases this year is certainly alarming.
"There are also several months to go before Hendra season finishes for the year.
"Our best option for dealing with this deadly disease is the Hendra horse vaccine currently in development. We're looking forward to the vaccine being available as soon as humanly possible."
He continued: "With the unprecedented number of cases across a vast area this year, it's clearly a national and urgent problem. Both flying foxes and horses travel large distances in Australia, and we believe all horses will need to be vaccinated to adequately protect against the disease.
"We think that vaccination should be a condition of entry into events, races and shows.
"An identification system through microchipping and keeping accurate records in a good database will be needed for us to be sure our patients have been vaccinated," Smyth said.
Horse owners can reduce the risks of Hendra virus in their horses by fencing off trees attractive to flying foxes, covering horse feed and water containers, and not feeding horses with food that could appeal to flying foxes such as fruit and vegetables.
They should wash their hands when dealing with horses, and contact a vet quickly if a horse is unwell.