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Spawning sockeye salmon are seen making their way up the Adams River in Roderick Haig-Brown Provincial Park near Chase, B.C. on Oct. 13, 2014.JONATHAN HAYWARD/The Canadian Press

The federal government has agreed to phase out 19 fish farms in B.C.’s Discovery Islands, following consultations in which First Nations raised concerns that wild salmon were at risk of disease and pests when they passed by fish farms in the area.

The Discovery Islands are a group of islands between Vancouver Island and the mainland and are on a migratory route for wild salmon.

Under the decision announced Thursday, Fisheries and Oceans Canada will issue licences to 19 Discovery Islands sites that had licenses that are expiring on Friday. The new licences are for 18 months, allowing for fish currently at the sites to be harvested and for all of the sites to be emptied by June 30, 2022.

After that, no new licences are to be issued.

“I’m feeling really wonderful today – because the hard work that was put in by an incredible team on this consultation is going to have benefits for the entire length of Fraser River and the Thompson River,” said Bob Chamberlin, who represented the Klahoose, Tla’amin and Homalco First Nations in consultations with the fisheries department.

The decision harks back to the Cohen Commission, a 2012 inquiry that looked into the decline of sockeye salmon in the Fraser River. It included a recommendation that Ottawa ban salmon farms in the Discovery Islands by Sept. 30, 2020, unless the fisheries minister was satisfied the farms posed a “minimal risk of serious harm to the health of migrating Fraser River sockeye salmon.”

In September, Fisheries and Oceans said its assessments concluded pathogens from fish farms posed a “minimal risk” to salmon in the area, resulting in an outcry from First Nations and environmental groups arguing that conclusion was flawed.

At the same time, the department announced plans to consult with seven First Nations with traditional territory in the Discovery Islands area, including the three that Mr. Chamberlin worked with, in relation to sites that were licensed to operate until the end of 2020.

In an interview Thursday, Fisheries Minister Bernadette Jordan said the decision to phase out the sites was difficult.

“This is impacting real communities and real people – and that’s not lost on me,” Ms. Jordan said. “But I also know that we have seven First Nations in the Discovery Islands who wanted to be part of the process, who wanted to be part of the discussion of what was happening in their territory.

“And it was important to me, and to this government, to make sure they were at the table as we went forward with this decision.”

The phase-out is designed to allow fish to be harvested and ensure an orderly transition process, the minister said.

Of the 19 sites affected by the decision, nine are already empty, with about three million fish in the other 10 sites.

“Nobody wanted to see us cull three million fish – that’s just not realistic. So we wanted to make sure there was a plan to transition that was fair to the industry. ... We wanted to give them the time they needed to make this transition in a fair and reasonable manner,” Ms. Jordan said.

In a statement, the B.C. Salmon Farmers Association said the decision puts salmon farming in British Columbia and across Canada at risk.

“This comes at a bad time, during a pandemic when local food supply and good local jobs have never been more important,” the statement said.

The group’s executive includes representatives from Mowi Canada West, Cermaq Canada Ltd. and Grieg Seafoods BC Ltd.

In a backgrounder included with its announcement, Fisheries and Oceans said the Discovery Islands sites are owned by Mowi, Cermaq and Grieg, as well as two unnamed smaller firms.

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