The Atlantic Salmon Federation and the Salmon Council of Newfoundland and Labrador say the escape last week in Hermitage Bay coincides with the wild salmon spawning season.
They say that increases the likelihood and severity of negative interactions between wild and farmed fish.
In a statement on its website, Cooke Aquaculture says high tides in the bay submerged the fish cage, freeing about 20,000 farmed fish.
The company says there is no threat to the environment, but provincial Liberal fisheries critic Jim Bennett says he's worried interbreeding between wild and farmed salmon could make wild salmon spawn less likely to survive.
The fisheries groups want the provincial government to develop and implement a monitoring program for wild and escaped farmed salmon on the south coast, where they say salmon production has more than tripled in the past decade.