The recall was sparked after anti-fish farming activist, Alexandra Morton, posted a photo of a lice-infested fish to the Sobeys Facebook.
"We did determine there was a problem with sea lice on a small portion of the whole Atlantic salmon that were pulled from our seafood cases and we've had some very direct conversations with our wholesaler and we're working through the process of how we can improve upon those quality controls," said Sobeys spokeswoman Cynthia Thompson.
Thompson refused to say how many of the roughly 80 fish had sea lice or where they were farmed.
Sobeys said it buys salmon from more than one supplier through its wholesaler, A.C.Covert & Sons.
The grocery chain plans to offer whole salmon again after the quality control issues have been fully addressed.
While not particularly appetizing, Health Canada said the parasite isn't harmful to humans.
Sea lice discovery incites debate
Sunday on CBC Radio's Maritime Connection, vocal fish farming opponent Karen Crocker urged Sobeys to keep the fish out of its stores. She said fish farming is polluting the coastal waters of Nova Scotia.
"Whether that be the feces, whether that be the excess feed, whether that be the pesticide used for sea lice, it all goes unchecked into the environment."
But Bruce Hancock, the executive director of the Aquaculture Association of Nova Scotia, expects the move by Sobeys will have little impact on the industry.
"We have to put this in context," he said. "What they removed from the shelves were whole salmon. It amounted to slightly more than 80 fish in all their stores, so it was hardly a major recall."
Hancock said sea lice exist all over the ocean.
Mitchell Moore, who works in the fish farming industry, is also coming to its defence. He said it's provided employment for him and allows him to support a family.
"We moved to a rural community, and now we're able to bring some money into that rural community and uplift that."