The future of Nunavut's $72 million turbot industry depends on the health of fish stocks but one company that fishes off the Baffin coast is accusing the competition of catching too many small fish.

"When the northern cod started to collapse, one of the things that people saw is that more and more small fish were being caught, and we don't want to repeat that," said Dave Bollivar with the Arctic Fishery Alliance.

The Arctic Fishery Alliance is one of four Nunavut-based companies with exclusive access to the turbot grounds in Baffin Bay, what's known as Sub Area 0A. 

Data there show an increasing number of small turbot are being caught, mostly by trawlers.

The Alliance fishes with gill-nets, which capture fewer small fish. Bollivar wants more research done to determine if trawlers are hurting the turbot population.

Jerry Ward is with the Baffin Fisheries Coalition, which uses trawlers and gill nets.

"We're very comfortable fishing at the current levels, maybe even a little more, based on the science," he said.

Ward said there's a downside to gill-nets, too. They catch more large, egg-bearing females.

There have been regular surveys by the federal Department of Fisheries and Oceans; they show stocks are stable in the surveyed areas.

There are rules for catching small fish in the turbot grounds off Baffin Island. The Department of Fisheries and Oceans can close areas to fishing if more than 15 per cent of the fish caught are under 45 centimetres.

In the northern waters of Baffin Bay, DFO's draft turbot management plan says small fish can make up to 48 per cent of the daily catch for trawlers.

But the Arctic Fishery Alliance says DFO is not enforcing those rules and DFO confirmed that in an e-mail to CBC.

Kevin Hill, a spokesperson for the Department of Fisheries and Oceans, says turbot stocks off the Baffin coast are healthy, and ongoing research shows the numbers in Baffin Bay and Davis Strait are stable.

The department says the small fish caught are monitored closely, and quotas for the area are conservative.