Seals are being shot at Scottish fish farms that supply salmon to UK supermarkets, including M&S and Waitrose - a supermarket which has long promoted its ethical and green credentials.

Licensed marksmen are hired to kill the seals by independent companies which say that the grey seal preys on their caged fish stock.

The seal slaughter was revealed by new statistics published by the Scottish government.

But a representative for Waitrose said that all major retailers source salmon from the same five Scottish farms which all work to the same standards.

A young grey seal pup pictured playing on the sand. The global population of grey seals is approximately 400,000, less than African elephant and a quarter of these reside in UK waters

Waitrose said that it is working with companies to limit seal deaths and it requires all its farmed salmon suppliers to take rigorous non-lethal measures to deter predators, including seals.

These include the proper use of acoustic devices, tensioned and weighted nets and the efficient removal of dead fish, which can attract seals.

The representative told MailOnline that seals breaching these non-lethal barriers 'can result in attacks on the fish, causing serious welfare problems.'

Marine Harvest admitted it killed 21 seals last year. The company supplies fish to Waitrose and Sainsbury's.

Steve Bracken, Business Support Manager of Marine Harvest Scotland told MailOnline that the company was disappointed by and regretted any increase in seal deaths.

'We are working hard to reduce the numbers through improved procedures and investment in new technologies.'

He said that seal deaths through culls have decreased substantially in recent years.

But Andy Ottaway, Campaign Director with the Seal Protection Action Group (SPAG) said that approximately 1,600 seals were reported shot in the past six years alone in Scotland and that this is still too many.

A Harbour seal looking straight into the camera while in the water offshore at a beach. Acoustic devices are being used in some waters to deter seals from trying to access fish farms

'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.

'They reported shooting 40 seals between them in 2016 out of a total of 75 shot by aquaculture, with 99 seals shot by all sectors in total,' he said.

He told the MailOnline that the grey seal is a lot less common than many people believe.

'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.'

A young grey seal pup plays on the beach. Although Scotland permits seals to be shot, a Seal Licence introduced in 2011 stipulates that they can only be shot with a permit

'The SPAG wants to see an end to seal killing and for the Scottish Salmon Industry to adopt strictly non-lethal methods to deter seals. Leading supermarkets can help by insisting their salmon suppliers stop killing seals.'

He said that using durable fishing nets with the right tension protects stock from seals.

'Fishing is a multimillion pound industry in Scotland and if shooting seals was illegal, the industry would have to invest in preventing seals from accessing stocks rather than just shooting them.'

Although Scotland permits seals to be shot, a Seal Licence introduced in 2011 stipulates that they can only be shot with a permit.

Seal culling had been widespread in Scotland and Mr Ottaway believes that this licensing law has helped to reduce seal shooting to its current record lows.

Around 1,600 seals have been reported shot under the scheme to date, an average of 300 each year.

Fish-farmers account for around half the total of seals shot and number of shootings has gone down by 70% from 240 in 2011 to around 75 in 2016.

Acoustic devices are being used to deter seals from trying to access fish stocks and although their are concerns that this could damage mammals' hearing, the technology has been improving.

Recently researchers from St Andrews University developed a device that only emitted noise when a seal came near the nets, so they didn't associate the din with an easy dinner.

It also allowed the sound to be set to specifically target different species without causing long-term hearing damage.

But that device was sold to a US investment firm so the technology is no longer held locally in Scotland.

Mr Ottaway said that the seals were entitled to remain in their environment.

'Seals are under a lot of pressure - from over fishing, culls, disease - and protecting them is an ethical issue.

'If the industry wants to sell fish they must be aware of the public reaction to their practices which many people find offensive and appalling.'

His organisation wants to see an end to seal culling and believe that this may be possible by 2020 as US legislation now bans imports from countries that allow killing sea mammals.

'So an import ban may be the reason that seal shooting is eventually outlawed in Scotland,' Mr Ottaway said.

Scientists also warn that culling is not the only threat that the UK seal population faces, having also been hit by phocine distemper, a fatal disease while the species also has to deal with depleting fish stocks, global warming and pollution.

A representative for Sainsbury's said the supermarket has the highest sourcing standards and sourcing with integrity was key to their work with farmers, growers and suppliers in the UK and all over the world.

'All our farmed salmon is responsibly sourced from RSPCA Assured farms, which use well-tensioned nets and acoustic devices to deter predatory seals.

'These deterrents are extremely effective and rarely fail. To ensure we're doing everything we can to protect seals, we were a founding member and the first supermarket to join the Salmon, Aquaculture and Seals Working Group, which is committed to safeguarding seals and this important industry.'