The results are expected on Friday afternoon.
"There have been seven or eight investigations in horses in the past, with Hendra virus excluded," said Dr Andrew Tomkins, director of biosecurity and product integrity with the territory's Department of Regional Development, Primary Industry, Fisheries and Resources.
The horse is located in Katherine.
Tomkins said today that the tests were being run at the Australian Animal Health Laboratory in Geelong.
He said a veterinarian called by the horse's owner noted that the animal had appeared to have received a blow to the head, and deduced that this was the cause of its bleeding, but as a precaution took samples to exclude Hendra virus.
Dr Tomkins said the samples were being tested despite the "very low possibility" of Hendra being present.
He said his department would hold a series of workshops in the near future to give veterinarians and local horse owners the latest information about the virus.
"In the meantime if any horse owner suspects their animal has the disease they should contact their veterinarian."
Three weeks ago, the department warned the territory's horse owners that Hendra virus infection had been shown to occur in fruit bats in the Darwin and Katherine areas.
There have no known cases of Hendra in horses or humans in the Northern Territory.
"All vets and horse owners should be aware of the risk of Hendra virus infection in horses and the risk of transmission of infection to people in close contact with infected horses," the department said.