They are one of Britain’s best-loved wild animals. But campaigners say they’re being systematically killed to satisfy our insatiable appetite for cheap salmon.

It’s claimed that as many as 5,000 seals are being shot every year by salmon farm operators around the Scottish coast. Under existing law it is quite legal for seals to be shot, as long as the approved type of rifle is used, and provided it is done outside the seals’ breeding season. 

With salmon farms established in almost every sea loch, seals have disappeared from many of their ancient haunts. Now MPs are demanding a change in the law to bring in an immediate ban on the deliberate killing of seals.

The slaughter of seals around our shores is reported by Countryfile’s John Craven for the first of a new series of investigations for the programme’s relaunch on prime time television tonight at 7pm. Andy Ottaway, director of the Seal Protection Action Group, told Countryfile: “The public are rightly outraged when they see pictures of seal pups being clubbed to death in Canada, but what people don’t realise is that there is a mass cull of seals around our coast in Scotland going on all year round. 

“It doesn’t get any publicity because it’s happening in remote locations where there are no witnesses - but this is the price we are paying for Scottish salmon.”

Salmon has become Britain’s favourite fish dish, with one million salmon meals now eaten every day. To meet that demand nearly 300 salmon farms have been set up in Scottish waters. The Hebridean Trust, a conservation group set up to protect seals and other wildlife around the inlets and islands of northwest Scotland, has monitored the decline in seal numbers in an area off Oban called the Lismore Special Area of Conservation. The group’s chairman, Mark Carter, who used to take tourists on seal-watching boat trips, said: “Four or five salmon farm cages have been set up in the area around Lismore Island, and over the past five years seal numbers have dropped by half.

“There’s a rocky islet called Dubh Sgeir to the northwest of Lismore where a salmon farm was set up right next to where the seals used to haul out. It’s been used by the seals for thousands of years, but now the seals have disappeared.”

There are no official figures on how many seals are being shot because salmon farm operators are not required to keep records, but campaigners claim that more than 3,000 are shot every year by marksmen employed by the salmon farms, and that at least another 1,000 are killed by salmon netsmen and anglers, shooting them around the east coast salmon rivers. 

Britain has internationally-important populations of two seal species, common and grey seals. Both species are being shot but mostly it is common seals, which are targeted because they tend to live and feed close to the shore where salmon farms and netting stations are located. This is particularly worrying for conservationists, because over the past eight years common seals in both England and Scotland have suffered a population crash, with UK numbers falling from an estimated 36,000 to 25,000. The decline has been described as “frightening” by scientists at St Andrews University’s government-funded Seal Mammal Research Unit. A senior research scientist at St Andrews, Callan Duck, said the cause of the decline was a mystery, though changes to sea’s ecology and falling fish stocks may be a factor. He said there may be some justification for shooting rogue seals which repeatedly broke into salmon cages, but the present law was too loosely defined.

“Repeatedly shooting animals that happen to be passing – or that are hauled up on rocky skerries and are not doing anything – I don’t think is acceptable,” he said.

Scott Landsburgh, chief executive of the Scottish Salmon Producers’ Organisation, said the number of seals being shot was being exaggerated, and that the true figure was less than 500.

He said seals kill 500,000 farmed salmon a year and that the industry needed to retain the right to shoot seals where this was unavoidable. “Shooting of seals is an act of last resort,” he said. “Let me put this in context. To begin with we take many, many steps before we even consider shooting seals – like net defences, net tensioners down below the water and acoustic devices used to scare the seals off.

“But a persistent aggressive rogue seal will still not be deterred and some seals won’t take ‘go away’ for an answer.”

At least one major supermarket, Sainsbury’s, has instructed suppliers to investigate the use of non-lethal methods to deter seals and is considering the introduction of seal-friendly salmon. Among ideas being trialled are acoustic deterrents and super-strong nets made of a fibre said to be nine times stronger than steel.

More than 120 MPs have signed an early day motion calling on the UK to recognise its international obligations to maintain its globally important seal populations, and calling for the introduction of a comprehensive ban on the killing of seals “as a matter of urgency.” Moves are also being made to incorporate better protection for seals within the Scottish marine bill.

Watch John Craven's report tonight at 7pm on BBC One. For more information about this week's Countryfile, click here.