A vaccine for horses that is designed to contain the deadly Hendra virus has now been made available in Australia.

Only that the vaccine, which is given to healthy horses, could be costly, Ben Gardiner, president of the Australian Veterinary Association (AVA), said, noting veterinarians could charge as much as between $130 and $220 for a dose of the new Hendra virus vaccine.

Developed by US pharmaceutical giant Pfizer along with CSIRO's Australian Animal Health Laboratory., Hendra virus vaccine is initially made available to vets in Queensland and northern NSW, states considered high-risk because of previous Hendra outbreaks. It took Pfizer two years to develop and perfect the vaccine's formula.

In Australia alone, more than 80 horses have died from the disease since it emerged in Brisbane in 1994. Twelve horses died in 2011. Human fatalities that have died from the deadly Hendra virus have been recorded at four individuals, all in Queensland.

"This vaccine significantly decreases the risk of exposure to Hendra virus for horse owners, handlers and veterinarians," Mr Gardiner said.

"The vaccine will also help to protect the health of horses and is a major win for anyone working in the equine industry, including veterinarians."

This is the first immunisation program ever made for the deadly bat-borne virus since 1994 its discovery, which was catapulted to the awareness of the Australian population when Vic Rail, a champion horse trainer, died from the illness in the Brisbane suburb of Hendra.

"For the first time, we have a specific control measure against a terrible virus which can make a healthy horse or healthy human mortality ill within 48 hours," CSIRO's veterinary pathologist Deborah Middleton told AAP.

"Because so far all human infections have resulted from sick or dead horses, this will break that cycle of transmission."

Batches of the vaccine are to be rolled out from Thursday.

Horses will be given a single shot followed by a booster within three weeks. Vaccinated horses that encounter live Hendra virus will have a very rapid immune memory response which will kill the virus before it has a chance to infect the animal, Dr Middleton said.

"I have seen first-hand how Hendra has created difficult working conditions for my colleagues and any Australian who works with horses," she said.

"A horse vaccine is crucial to breaking the cycle of Hendra virus transmission from flying foxes to horses and then to people, as it can prevent both the horse developing the disease and passing it on."