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Mowi said it would focus production on “locations more appropriate for modern day aquaculture”.
The closure of the Loch Ewe salmon farm comes after 15 years of failing to meet certain environmental standards, with the Scottish Environmental Protection Agency (SEPA) reportedly imposing reductions of around two thirds on the permitted quantity of fish farmed.
Another farm at Loch Duich is also set to close.
Both are in inland sea lochs which have been blamed for adverse impacts on marine life.
Mowi said it had identified the farms “as candidates for relocation due to the enclosed nature of the sea lochs where the farms are situated and the sites’ proximity to sensitive wild salmonid habitats.”
Experts said the closures could have ramifications for the wider industry, which is already under pressure to deal with surges in sea lice affecting stocks and mass mortality events because of algal blooms in warming waters.
Other farms “will be at serious risk now, because the regulator should continue to apply reductions as and when they fail,” campaigner Corin Smith told The Independent.
Mr Smith’s freedom of information (FOI) requests have previously revealed the Scottish government’s support for salmon farming expansion.
The Loch Ewe farm has recorded “unsatisfactory” benthic levels every year since 2005. Benthic monitoring measures the levels of macro-invertebrate species in and on the seabed.
Andrew Graham-Stewart, director of Salmon and Trout Conservation Scotland (S&TCS), said: “We welcome Mowi’s decision to close the Loch Ewe farm. There can be no doubt that the decision is a vindication of S&TCS’ long campaign to end salmon farming in this enclosed sea loch,” which the organisation said “has devastated sea trout stocks in iconic Loch Maree, previously the best sea trout fishery in western Scotland”.
He said they believed “the other factor in Mowi’s decision is clearly the farm’s failure to reduce its benthic impact.”
He added: “As a consequence, SEPA has cut the farm’s permitted biomass very substantially, thus diminishing its commercial viability.”
Mowi has “signalled its intention to move the biomass elsewhere,” he said, adding: “If Mowi wishes to apply for a biomass increase at another location, then that should be judged on its own merits. Indeed, it would be disingenuous to try and link it to the closure of Loch Ewe. Furthermore it is vital that any biomass increase elsewhere avoids migration routes for wild salmonids.”
But Mowi said in a statement the sites’ permanent closures would only come if they could relocate the salmon to its other farms.
It added: “The sites will be closed permanently conditional to the support from our regulatory system to transfer the biomass to other locations, and to sustainably expand our production in the best possible areas for salmon farming thus protecting the associated jobs.”
Mr Smith said this stance was “ridiculous”.
“It is significant that Mowi are saying it’s an internal decision and they’re making it conditional on the biomass being relocated. It’s a thoroughly empty statement because the idea the law would permit the unilateral transferring of biomass from one farm to another on the basis of the original farm failing its environmental standards is ridiculous,” he added.
He said he believed the “idea that Mowi could take non-compliant biomass and dump it somewhere else is an absolute nonsense.”
The “relocation” plan comes months after claims Mowi had misreported the volume of chemical medications it uses to fight disease at its Scottish salmon farms.
In April, the company revealed the amount of gutted salmon it produced from Scottish waters had fallen by 36 per cent in a year, with infestations of sea lice and disease blamed.
Marine ecologist Sally Campbell told The Independent: “There’s clearly a serious problem up the west coast now with sea lice.”
She added: “The tragedy is the little smolts from the wild salmon come down through the fresh water to the sea to go out to sea for three years, they swim past these fish farms and their gills and scales are less robust than they are once they’re bigger, and they pass through the sea lice and it’s thought are responsible for the deaths of a lot of the smolts.”
Speaking about the challenges the industry now faces, Ms Campbell said: “They’re under quite a lot of pressure now, because over the last couple of years a lot of us up the west coast hear what’s going on. There’s been a lot of news about companies taking away dead fish and people smelling dead fish coming from huge ships.
“My concern is the ecosystem is being damaged beyond repair. Many chemicals are used to inhibit the lifecycles of the sea lice, which are from the same group of animals as prawns, crabs and lobsters.”
She said the salmon companies public relations teams would say: “We’re going to look after the sea lochs.”
But she said they would ”look after their own interests in the short term. “
She added: “The industry will kill itself at the rate it’s going.”
Alastair Sinclair, the national coordinator for the Scottish Creel Fishermen’s Federation told The Independent: “My impression of the whole thing is that up until we had salmon farms in the sea lochs on the west coast, we had problems, but not to the degree that we do now. “There’s only one suspect in the grand scheme of things – that’s the salmon farming industry.
“They should not be using west coast sea lochs, due to the chemicals, it’s unnatural. It’s polluting the seas the way the Victorians would pollute the waterways without any thought of consequence.”
Managing director of Mowi Scotland, Ben Hadfield, said: “Mowi has strived to improve relations with the wild fish sector and has been clear that it will seek to expand its operations in Scotland, whilst securing reduced impact on the environment and further developing the significant economic contribution that it makes to rural Scotland.”
The Independent has contacted SEPA for comment.