The Department of Fisheries has been ordered to shore up its regulations to prevent infections from being transferred from dozens of fish farms to the open marine environment.
The legal action was prompted by elevated concerns about one particular illness that attacks the heart and muscles of salmon, which the court heard could imperil the Fraser River sockeye.
The advocates hailed the Federal Court decision on Thursday that struck down a portion of the rules governing the transfer of fish between aquaculture farms. The court gave the department four months to draw up new regulations.
The case hinged on whether B.C.'s prolific coastal salmon farming industry is allowed to make the decision to move diseased fish into its netted pens in the Broughton Archipelago between Vancouver Island and the central coast, said biologist Alexandra Morton.
"Which unfortunately are along our wild salmon migration routes," she said. "So all the viruses in the pens, of course, can get out of the pens."
It was Morton, a vocal fish-farm opponent, who identified inconsistencies between two sets of aquaculture policies and initiated the judicial review.
"We've learned this with chickens and pigs and cows, with all the avian flu, swine flu, mad cow. You don't let pathogens go back and forth like this."
The legal action stemmed from accusations by Morton that a fish farm operator had trucked diseased salmon smolts from its Dalrymple hatchery to its Shelter Bay fish farm.
Samples of the smolts bred by Marine Harvest Canada tested positive for a virus called piscine reovirus, or PRV, in June 2013, the court heard.
In his ruling made Wednesday, Judge Donald Rennie stated the "weight of expert evidence" supported the view that PRV is the viral precursor to heart and skeletal muscle inflammation in salmon. He wrote the virus has recently been discovered in Canada.
Marine Harvest, which bills itself as B.C.'s largest salmon aquaculture company, disputed that it has ever transferred unhealthy fish. Therefore, said spokesman Clare Backman, the voided clauses aren't important to company operations.
"We don't find the decision changes anything in our ongoing business day-to-day."
Backman said the company provided evidence to court of the presence of PRV along the B.C. coast existing long before salmon farms. The company also claimed it is naturally occurring and not linked to any disease at all.
The Department of Fisheries said it was reviewing the decision, but noted the ruling pertains to two subsections of 140 licence conditions.
The DFO website states that examination of hundreds of fish has found no evidence to date of the disease in wild or farmed fish along the coast.
The department's lawyer told the court that as many as 120 licences due to expire by the end of 2015 could be affected by the invalidated regulations.
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