Calf exports are being routed on a bureaucratic merry-go-round which is increasing transport times by up to nine hours in some cases, exporters have claimed.
The live shippers maintain that new restrictions on mixing loads of calves from the Republic and Northern Ireland have caused serious logistical problems.
"If I purchase calves in Northern Ireland, calves from the South cannot be added to the lorry on the way to the ferry at Rosslare," said one leading shipper, who did not wish to be named.
"The calves from the South have to be transported separately, which does not make sense.
"There is a crazy situation operating with different regulations in the two jurisdictions.
"I am not allowed to add Southern calves to a lorry carrying calves from Northern Ireland, but there is no difficulty in adding calves from the North to a lorry carrying Southern calves.
"To avoid having to use two lorries, I have to load the calves in the South first, travel to the North to load the calves there, and then travel back to Rosslare," the exporter claimed.
"It is adding eight to 10 hours to the transport time for the Southern calves.
"This extra travel time, which is bureaucracy gone mad, is defeating the objective of good animal welfare, which we are all encouraged to adhere to."
He said that once the calves reach the port there is no problem with mixing them.
A spokesperson for the Department of Agriculture did not disagree with the outline of the procedure.
He explained that calves from both jurisdictions could travel together, but only in sperate trailers being towed by the same truck.
"In the event of an outbreak of disease subsequently attributed to animals from one jurisdiction, this affords protection for animals from the other jurisdictions."
Live exports of calves boomed to a 20-year record last year. Almost 160,000 calves were exported last year, compared to 123,000 in 2009.