The dogs were recovered by gardaí from the Waterford City Roads Policing Unit, assisted by Waterford Animal Welfare (WAW) on Thursday.
WAW said the dogs were seized as both their ownership and destination was “questionable” and “could not be proven".
All of the dogs were un-spayed females of different breeds. It is thought they may have been picked up throughout the Munster region.
All have received health checks since being recovered and are being cared for by WAW.
One of the dogs has since been reunited with her owner as a result of microchipping.
Andrew Quinn, chairperson of WAW, said the organisation had been forced to rent kennel space for the dogs as they are overrun with animals.
He said the remaining five dogs are safe and well in the care of WAW, who are now seeking their owners.
Following posts on social media, he added the organisation had received many calls from people believing themselves to be an owner, but that absolute proof of ownership would be essential before any of the dogs could be handed over.
Gardaí are continuing to investigate the case.