The Ministry for Primary Industries says it may never know the origin of a neurological strain of equine herpes which has so far killed seven thoroughbred horses.
The virus - a neurological strain of the common equine herpes virus type 1 - has struck in New Zealand for the first time, killing seven mares and leaving another six infected at a Waikato stud farm.
The farm is in lockdown. Authorities are refusing to name it, citing privacy concerns.
Andre van Halderen, principal adviser at the Ministry for Primary Industries, said the virus was difficult to diagnose and confirm which made the source hard to track.
"It could have come in at some stage through an imported horse or it could be a mutation that arose here," Mr van Halderen said. "I'm pretty sure we'll never be able to pin-point where it came from."
Thirty other mares that had been in contact with the infected dozen were segregated from the rest and were being monitored for any possible symptoms.
Mr van Halderen would not name the stud farm at the centre of the outbreak for the owner's sake.
"We do that as a matter of a principle."
However, Neil Clarkson, news editor of horsetalk.co.nz, said it was important owners knew who had been in contact with their horses.
"My initial concern would be looking after my horses in terms of being careful who was [given] access to them."
Mr Clarkson said the outbreak was concerning and economically damaging to the industry.
"We would have to be buoyed that the Ministry for Primary Industries indicates that the situation is under control, but at the end of the day the neurological form of EHV1 is a very nasty form of the disease."
Michael Martin, chief executive of the Thoroughbred Breeders' Association, was confident that the outbreak had been dealt with appropriately.
"Everybody in this industry for years has been conscious of quarantining and [knowing] how important animal health is in New Zealand," Mr Martin said.
The stud farm in question will be under quarantine for at least 21 days. However, if a new case is confirmed that will be extended.