This artificially coloured electron micrograph of Hendra virus is from the first identified case in Brisbane in 1994. © CSIRO
The Anglo-Arab filly from J4S Equine Nursery at Cawarral, east of Rockhampton, owned by John and Christine Brady, died on Saturday.
Queensland Primary Industries Minister Tim Mulherin said today that testing had confirmed Hendra virus.
Two other horses have died in the past two weeks, but those deaths are understood to have been the result of old age and a snake bite.
The virus is carried by fruit bats and the risk appears greatest during the bats' breeding season.
Last August, Brisbane vet Ben Cunneen died in hospital following an outbreak among horses at the Redlands veterinary clinic. A vet nurse also was infected, but recovered.
There have been 11 known outbreaks of hendra among horses, with four resulting in cases in people. Half have proved fatal.
While people have caught the virus from horses, there has yet to be any evidence of human to human transmission.
Queensland Health officials are monitoring the health of workers at the stud.
Mulherin said the infected horse had shown classic Hendra symptoms, which include nasal discharge, a fever and deteriorating health.
The stud and an adjoining property are under quarantine.