The federal government says it's phasing out fish farms along a key wild salmon migration route in British Columbia waters within the next 18 months. 

Fisheries Minister Bernadette Jordan says 19 fish farms in the Discovery Islands near Campbell River are being issued licences that expire on June 30, 2022, and she does not intend to renew them.

"It was a very, very difficult decision, this is not something that I took lightly, recognizing coastal communities will be impacted by this," Jordan said in an interview. 

The government made the decision after consulting seven local First Nations opposed to the farms. The federal government is committed to working with the industry on a "fair" transition to sustainable aquaculture, she said. 

The licences for the 19 farms were set to expire Friday. Nine of the farms have no fish, and Jordan said her intention is that the remaining 10 will not be permitted to add fish to the pens. 

All farms should be free of fish by the time the licences expire, but existing fish at the site can complete their growth cycle and be harvested, Jordan said. About 80 per cent of the fish are expected to be harvested by April.

Environmental advocates have long argued that the open-net pen farms host parasites and diseases that can spread to already struggling wild salmon stocks.

Stan Proboszcz, science adviser for Watershed Watch Salmon Society, described the Discovery Islands as a "migratory bottleneck" for wild salmon. 

"The area is comprised of narrow channels where these farms are located, so the fish migrate really close to the farms and they can spread parasites and diseases to the wild fish and have population impacts," he said. 

Proboszcz said juvenile salmon begin migrating through the area in April as he questioned the length of time it's taking to close the farms, adding if an election were held in the meantime a new government could stop the plan. 

"This has been a long time coming and I think it's a time to celebrate with caution," he said. 

In 2012, the Cohen Commission into the Decline of Fraser River Sockeye recommended phasing out fish farms in the Discovery Islands by Sept. 30, 2020. 

Although that deadline has passed, Jordan says there are fish currently on the farms and the government wants the phase-out to be fair and reasonable. 

"I don't think anyone wants to see us cull three million fish," she said.

In September, the Department of Fisheries and Oceans said nine pathogens from farmed salmon in the Discovery Islands pose a minimal risk to wild salmon, based on its scientific assessments. Some conservation groups criticized the department for not doing an assessment of sea lice. 

The BC Salmon Farmers Association said the decision has significant implications and puts salmon farming in B.C. 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," it said in a statement, adding it will speak with its members before commenting further.

Phasing out net-pen fish farming in B.C. by 2025 was a Liberal campaign promise in the federal election. 

Government figures show there are about 130 marine finfish farms in B.C. and the vast majority raise Atlantic salmon. They are concentrated in the Campbell River, Port Hardy and Tofino areas around Vancouver Island. 

Jordan said the process for phasing out the remaining farms by 2025 will be different than what's being done in the Discovery Islands and parliamentary secretary Terry Beech will begin consultations in January.

Homalco Chief Darren Blaney said the news is a relief to members of the First Nation. 

"It feels like it's been such a long time, you know, to watch our salmon dwindle and dwindle and our community get less and less food fish each year, it was hard to bear," Blaney said from Campbell River. 

The Homalco, who are known as the "people of the rapids," have a history and culture linked to the salmon and the waters they run in, Blaney said. 

Fish farms are one of several threats facing the salmon, including climate change, warming waters and habitat loss, he said. Members of the First Nation are working to restock local river systems through a stewardship program. 

"The thing about salmon is they're resilient and if we give them a chance and a little bit of support, I think we'll build them back up."

This report by The Canadian Press was first published Dec. 17, 2020.

Amy Smart, The Canadian Press