"A total of 46 horses, including showjumping, dressage and eventing horses are making the long-awaited journey home, after being provided permits from Victorian authorities," NSW Primary Industries Minister Ian Macdonald said.
The animals have been stuck in NSW since August 25.
Their release to travel into Victoria comes hot on the heels of the first thoroughbred horses crossing the Murray River on Monday night.
"Victorian authorities have approved the transport of 46 pleasure horses belonging to 30 owners, including ponies, showjumpers and animals owned by Charles Sturt University equine science students," Mr Macdonald said.
"Also, a few of the horses caught in the Condobolin showground lockdown when the horse flu outbreak began are amongst those finally being able to return home."
Mr Macdonald said for the past 14 days the horses have been in quarantine on seven NSW properties. They will be required to spend a further seven days in quarantine in Victoria at Werribee.
"All of these horses have come from the NSW green zone which is free of horse flu. None have been infected or vaccinated and all have tested negative for the disease," Minister Macdonald said.
"The horses will cross the Murray River in truckloads at five points between East Gippsland and Echuca over two days."
The movement of horses into Victoria without a permit is illegal, he added.
"Offenders who attempt to illegally bring horses across the border face fines of up to $A24,000 and two years imprisonment."
He said the horses and vehicles had to meet stringent requirements to obtain approval from Victorian authorities.
"The floodgates have not been opened to allow uncontrolled movement across the Victorian border.
"Victoria only allows limited movements on permit following quarantine and testing, and the adoption of tough biosecurity during transport."