The positive test adds fuel to the argument of the pro-vaccination lobby which believes Australian racehorses should receive ongoing jabs.
New South Wales Primary Industries Minister Ian Macdonald told the conference a horse was undergoing a third test today after returning both a positive and negative result in two earlier tests.
The horse is being housed at the Eastern Creek quarantine facility, from which the virus escaped last August, costing horse interests hundreds of millions of dollars.
A subsequent review resulted in a major overhaul of Australia's quarantine operation.
Mr Macdonald is recommending voluntary vaccinations of all horses in the state.
However, ongoing vaccination is opposed by the Australian Veterinary Association (AVA) and the Australian Horse Industry Council, both of which believe ongoing vaccination would make containment of future outbreaks more difficult because vaccinated horses may be infected but not show obvious symptoms.