More than a dozen dogs were seized at Rosslare Europort on Monday night.
A total of 17 animals were found on a transporter set to board a ferry to the UK.
Revenue officers, as well as members of the gardai, ISPCA, WSPCA and the Dog Warden from Wexford County Council took part in the operation.
The ferry was heading from Rosslare to Fishguard in Wales, and the ISPCA believed that they did not all have pet passports, as required by law.
Among the breeds that were found in the cages were terriers, pugs, spaniels, collies, hounds and labradors.
All of the dogs were transferred to the Wexford Society for the Prevention of Cruelty to Animals and the Wexford Dog Warden.
Further investigations are still ongoing.
A garda spokesman said: "Last night in a joint operation involving Revenue Officers, An Garda Síochána, ISPCA, WSPCA and the Dog Warden from Wexford County Council, 17 dogs were seized at Rosslare Europort.
"The dogs were discovered as a result of routine profiling, during a search of an Irish registered transporter booked to board the ferry to Fishguard, Wales.
"All dogs were transferred into the care of WSPCA and the Wexford Dog Warden and follow up investigations are ongoing."
An ISPCA spokeswoman added: "The dogs, a mix of breeds including Terriers, Pugs, Spaniels, Collies, Hounds and Labradors were initially cared for by the Wexford Dog Warden Service. The ISPCA would like to thank our affiliated member Wexford SPCA and the various agencies involved in last night’s seizure.
"The dogs will be transported to the ISPCA’s National Animal Centre once they have been assessed by a veterinary practitioner.
"ISPCA Inspectors will be liaising with customs officials to investigate the matter and to establish what potential offences may have been committed. None of the dogs will be available for rehoming at the moment.
"This is the second large scale seizure of dogs involving the ISPCA within a week. Last Thursday four puppies, two pregnant dogs and nine other adult dogs were seized by the ISPCA along with two cats and their litters of kittens in a pre-planned operation with Gardaí in the Midlands."
