Police allege the man jumped the border late at night on September 28 via a back route near Bombala, taking two riding ponies to a property at Heyfield, 200km east of Melbourne.
The man has been summonsed to appear in Queanbeyan Local Court on December 3.
Victorian authorities are also investigating related offences in Victoria.
Deputy chief veterinary officer Ian Roth said the man was traced by rural crimes investigators following a report of the movement which included number plate details.
"The movement resulted in a Victorian property being placed in quarantine, the testing of horses for equine influenza and the controlled return of the horses to the Canberra property," he said.
Meanwhile, charges relating to an illegal horse movement in the north-west of the state during September were mentioned in the Inverell Local Court on Thursday.
Magistrate Gordon Lerve adjourned the matter for hearing in the Boggabilla Local Court on December 5.
Police allege a 47-year old man moved a horse during the horse standstill imposed by NSW Department of Primary Industries following the outbreak of equine influenza.
He was charged with having breached a control order issued under the Exotic Disease of Animals Act 1991.
Police continue to investigate a number of potentially illegal horse movements.