Wild salmon campaigners in British Columbia are claiming victory after the Federal Court struck down licensing rules that allow fish farms to transfer diseased fish into open ocean pens.

The ruling came after a lawsuit filed by biologist Alexandra Morton and Ecojustice argued that federal aquaculture licensing was inconsistent with the law protecting wild fish and the marine environment.

The Ministry of Fisheries and Oceans licensing allowed fish farm company Marine Harvest to make its own decisions surrounding the transfer of farmed fish carrying viruses that may harm wild salmon, into open ocean pens.

'Playing biological roulette'

"This was a reckless practice that put wild salmon at risk by exposing them to potentially dangerous disease agents," Morton said in a statement.

"The Court's judgement comes as a big relief. Salmon farms are just nets or cages open to our oceans. To stock them with farmed fish carrying viruses is playing biological roulette.

"It cannot be left to these companies to decide whether putting farmed fish carrying viruses into the ocean environment is safe."

Inflammation of heart muscles

Morton and Ecojustice filed the lawsuit in 2013 after piscine reovirus (PRV) was found in fish held in Marine Harvest's Dalrymple hatchery, on the migration route of Fraser River sockeye.

The disease has been found to cause inflammation of the skeletal and heart muscles of salmon.

Judge Rennie ruled that the specific licensing regulation under examination is inconsistent with the broader protective regulatory pre-conditions.

He declared it invalid, awarding a four-month suspension of judgement to cover the upcoming salmon migrations.

The Ministry of Fisheries and Oceans said that as many as 120 licenses, due to expire at the end of the year, could be affected.

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