AGRICULTURE Minister Simon Coveney says his department has removed the right to issue horse passports from one organisation.
In the wake of the horse burger controversy, the minister said there have been a "small number of complaints" in the area of horse traceability.
He said two compliance notices were issued to horse slaughtering plants in the past two years.
Mr Coveney said since 2009, every new horse has to be microchipped and issued with a matching passport.
He said seven different bodies were able to issue equine passports.
But the Department of Agriculture has removed the right from one organisations, the Irish Cob Society, because it was "not happy" the procedures expected would be fully implemented.
Fianna Fáil agriculture spokesman Eamon O Cuiv said there were many horses pre-dating the 2009 deadline.