Marine Harvest Canada disputes the ruling made last month that struck down a portion of the regulations governing the transfer of fish between aquaculture farms.
The Department of Fisheries has also appealed the decision, which deals with two sub-sections of one licence condition among about 140 conditions for marine aquaculture facilities.
The court heard samples of salmon smolts bred by the company tested positive for a virus linked to heart and muscle damage, but Marine Harvest argues the disease has never been detected in Canada.
The company adds the virus is known to be relatively common and benign and that it existed in B.C. before salmon farming.
Ecojustice lawyer Margot Venton, whose group launched the successful judicial review, says the Federal Court's direction was clear — the licence conditions were unlawful and not based on science.
The legal action stemmed from accusations by fish-farm opponent Alexandra Morton that Marine Harvest had trucked diseased salmon smolts from its hatchery to a coastal fish farm in the Broughton Archipelago.
The court ordered the department to draw up new regulations within four months.