The court was told he moved two riding ponies interstate to Victoria via a back route near Bombala.
"The man used a horse float to illegally move two horses from Murrumbateman in NSW to Victoria on 28 September," Primary Industries Minister Ian Macdonald said.
"The man was fined for contravening an equine influenza control order under the Exotic Disease of Animals Act 1991.
"When the rest of the horse industry was working hard to stop the spread of EI this man was undermining their effort and the whole eradication campaign."
Mr Macdonald said if the horses were infected with the flu, the illegal movement could have potentially spread equine influenza into new parts of NSW and also Victoria, which is free from horse flu.
"This is a timely reminder that that there is no room for complacency when it comes to this contagious disease," he said.
"The NSW DPI continues to work closely with NSW Police Force Rural Crime Investigation Unit to monitor compliance of existing regulations on horse movements."