Activists claim it has failed to force firms to comply with aspects of the law, which permits seals to be shot at some of the near-300 salmon farms in Scotland as a last resort to avoid damage to supplies bound for supermarkets and shops.
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They claim it is sentencing some pups to starve to death if their parents are killed because shooting is permitted through the breeding season.
The Seal Protection Action Group said the law, which makes clear that seals can only be slaughtered if all other methods of controlling them fail, is being abused, and is considering a legal challenge to the Government’s application of the law.
In total, 65 licences have been granted since the Marine (Scotland) Act came into force last week, allowing the deaths of 1298 seals.
Spokesman Andy Ottoway said it “beggared belief” that the multimillion-pound industry could not keep predators away from salmon without shooting them.
He said: “Forty years ago we stuck a man on the moon, so surely we can find a way of keeping seals out of fish farms. If it was whales or dolphins it would be banned overnight.”
The Scottish Government said it has strict enforcement rules for the issuing of licences. However, 66 applications have already been granted including one for a yet-to-be-completed fish farm.
Campaigners argue that shooting should be a last resort, only reached where non-lethal methods have been exhausted. In a publication covering its seal-shooting policy, the Scottish Government states that not all licencees are using these measures.
“The majority of seal licence applicants are either using or have investigated the use of non-lethal measures,” it states.
A Scottish Government spokesman added: “Marine Scotland assess all fish farms before granting a licence to ensure that non-lethal measures, as appropriate to that site, are being taken. These include tensioned and predator nets, acoustic deterrents and seal blinds.”
The Government notes that, in many cases, “the measures used ... appear to have proved unsatisfactory in that they have not entirely eliminated the risk of seal predation”.
Campaigners called on the Government to phase out shooting licences to give the industry a “mandate to come up with measures to stop the killing of seals”.
Fears have also been expressed about the potential impact on tourism.
Marine biologist David Ainsley, owner of the Sealife Adventures attraction in Oban, Argyll, said that farms shoot seals “not as a last resort but simply because killing is the cheapest solution”.
Caroline Warburton, of Wild Scotland, which represents more than 90 outdoor tourism firms, said: “The wildlife tourism sector in Scotland has grown significantly over the last 10 years and many coastal and marine tourism operators include seals as part of their trips or promotions. A number of our members have voiced concerns about the shooting of seals in their area and should seal numbers drop significantly Wild Scotland is concerned that livelihoods would be affected.”
Scottish Green Party co-convenor Eleanor Scott said the party had worked in the last parliament to ban “this outdated and brutal licence regime”. She added: “The scale of this killing spree is a surprise even to us.
“The fish farming industry could just install double nets to protect their fish, but it appears it’s cheaper for them just to reach for the gun, even in the breeding season.”
Labour and the Liberal Democrats said there were circumstances where seals could reasonably be killed as a last resort, but only if they posed a serious threat.
Government, industry and charity bodies are now working to improve non-lethal measures to protect against seals.
Mr Ottoway said he was speaking to the animal protection bodies, the SSPCA, Freedom Foods, Sainsbury’s, which uses significant amounts of Scottish salmon, and Marine Harvest, the country’s largest salmon farmer.