"This is the first time outside of a laboratory that an animal other than a flying fox or a horse, or a human, has been confirmed with Hendra virus infection," Queensland state Chief Veterinary Officer Rick Symons said.
So far, 14 horses have died or been put down in Australia since June as a result of the Hendra virus, which was only discovered in 1994.
No humans have yet been infected in the current outbreak, which has affected farms in New South Wales and Queensland, but four of the seven people ever to have contracted the disease have died.
Symons said the dog, which tested positive for antibodies for the disease but appeared healthy, was on a property where Hendra had been confirmed and was currently under quarantine.
He added that the case raised many questions for biosecurity and health officials and researchers.
"We don?t know how the dog contracted the virus or when it happened," he said.
"Based on our knowledge to date, it is most likely that the dog caught the virus from an infected horse."
The virus is thought to be spread to horses via half-chewed fruit, or water and food contaminated by bats' droppings.
Malaysia has imposed a ban on the import of horses from Australia as a precautionary measure following the outbreak.