Salmon farms in Scotland are protected by licensed marksmen who shoot seals that threaten fish stocks.
The farms are run by independent companies and employ the shooters to kill common and grey seals which are said to pose a risk to caged salmon.
See also: Farm salmon 'should be sterilised'
Marine Harvest is one company that uses marksmen and appeared in new figures released by the Scottish government, which allows the culling of seals.
Waitrose, M&S, and Sainsbury's source salmon from Scottish farms in which seal culling is practised, according to The Times. It arguably brings the ethical credentials of the higher end supermarkets into question.
Salmon is one of the most popular fish in the UK
Marine Harvest, which supplies Sainsbury's and Waitrose, together with M&S supplier Scottish Sea Farms, reportedly shot 40 seals last year. The animals are known to attack fish stocks. Just 400,000 remain in the world's oceans, campaigners say.
Waitrose, which has long championed its green policies, made assurances that it is working with companies to limit seal deaths. The supermarket and it 'requires all its farmed salmon suppliers to take rigorous non-lethal measures to deter predators, including seals'.
Acoustic devices are deployed in waters around salmon farms, as well as tensioned, weighted nets, and the efficient removal of dead fish.
But seals have been known to breach non-lethal barriers – and that's when seals might be shot. Marine Harvest admitted shooting 21 seals last year, The Times reports.
Waitrose takes salmon from Marine Harvest
Andy Ottaway, Campaign Director with the Seal Protection Action Group (SPAG), said that approximately 1,600 seals were reported shot in Scottish waters over the last six years.
"The companies shooting the most seals are Marine Harvest who supply Sainsbury's and Waitrose, and Scottish Sea Farms who supply Marks and Spencer's," he said.
"There are fewer grey seals than African Elephants in the world, but because they are concentrated in UK waters, people believe that they are thriving."
"I don't think that the public knows that seals are being shot just so that they can eat salmon."
Farmed salmon has become increasingly popular in recent years due to high demand for the fish, alongside depreciating levels of wild salmon. The WFF says wild Atlantic salmon are in 'crisis'.
An Atlantic grey seal
Seal culling has been long practised in Scotland, just as the culling of other animals takes place in agricultural and environmental sectors across the UK.
Ben Hadfield, managing director of Marine Harvest's Scottish operation, told The Times: "If seals keep attacking the fish, then, like a farmer kills foxes, we shoot them."
Hadfield also said that the numbers shot had reduced from more than 100 a year.
Mirror Online has contacted the three supermarkets mentioned for comment.