Biosecurity Queensland says a horse has tested positive to the bat-borne lyssavirus, in what is believed to be the first cross infection of its kind.
Authorities have quarantined a property on the southern Darling Downs.
The animal fell sick at a southern Darling Downs property and was put down about a week ago.
The property has been quarantined.
Another 20 horses on the property are being tested and monitored, and people who had contact with the infected animal are being offered preventative treatment.
Another horse from the same property was euthanased five days earlier, but it was not tested for lyssavirus.
Chief biosecurity officer Dr Jim Thompson says it is not clear how the horse contracted the virus, but there had been small bats in the area.
"For rabies or for lyssavirus, it's usually related to a bite or a scratch, so it's a much closer interaction in the past," he said.
"It's too early to tell how that may possibly have occurred."
Lyssavirus is similar to rabies.
Chief health officer Dr Jeannette Young says it is important to remember that human cases of lyssavirus are incredibly rare.
"There have only been three recorded cases in Australia, all in Queensland, and sadly all three people passed away," she said.
"All three cases were the result of direct exposure to bats with lyssavirus.
"This is the first case where Australia bat lyssavirus has been identified in a horse, although we know from overseas that horses can be infected with rabies.
"We do, however, have a preventative treatment that is effective in any person not displaying symptoms of the virus."
Previously, horses in Queensland and New South Wales have died from another bat-borne disease, Hendra virus.
It was first discovered almost 20 years ago, and has caused the deaths of three people known to have contracted the disease.