The Ministry for Primary Industries says it is confident only one farm in Waikato has been affected by the equine herpes virus.
It is the first time the neurological form of the disease has been detected in New Zealand, although the illness has infected horses in the United States, Europe and Australia in the past.
The ministry says 12 horses were infected and six have either been put down or have died.
Its deputy director general compliance and response, Andew Coleman, says the property has been proactive in preventing the spread of the virus.
Mr Coleman says the virus can cause paralysis and incontinence.