Despite stipulations that carcasses should be recovered where possible for examination, the majority of carcasses are lost and over 97 per cent of seals killed were not subjected to a post-mortem.
Between 2011 and 2015, 1531 seals were killed by salmon farms, salmon netting stations and angling groups, yet only 91 carcasses were recovered.
The information came to light following parliamentary questions to the Cabinet Secretary for the Rural Economy and Connectivity, Fergus Ewing MSP, from Scottish Green Party MSP Mark Ruskell.
Under the licensing system which allows seals to be killed in Scotland, carcasses should be recovered and sent for post-mortem.
Post-mortems are critical to determining the extent of suffering endured by the seal before death.
However, only 91 (six per cent) of carcasses were recovered and just 40 (2.6 per cent) had a post-mortem.
Harry Huyton, director of OneKind, a Scottish charity working to end cruelty to animals, said: “Whilst we understand that safety must come first and therefore many carcasses cannot be recovered, the extremely low recovery rate is surprising and disappointing.
“It also suggests that many seals are being shot whilst in the water, which risks prolonged deaths and injury.”
Mr Ruskell, the Scottish Green Party’s spokesman for climate, energy, environment, food and farming, said: “It is shocking that there is such a low rate of carcass recovery and post-mortem on seals killed by the fishing industry.
“These are crucial steps in preventing unnecessary suffering and pain to Scottish seals. I urge the government and fisheries across Scotland to step up and reinvigorate their commitment to increasing carcass recovery and post-mortem rates.”
Of the 40 post-mortems that were carried out, the Cabinet Secretary has confirmed that 36 seals died ‘almost’ immediately.
Mr Huyton added: “‘Almost’ is a very vague term and does not rule out suffering. We are calling for clarification as to how long it is taking shot seals to die.
“Furthermore, of these 40, the Cabinet Secretary confirmed that the post-mortems suggested welfare concerns for two seals and uncertainty for another four.
“OneKind is calling for the Scottish Government and the fishing industry to continue to phase out seal shooting, with a target of ending it entirely by 2020.
“Until then, we want to see a fresh commitment to increasing carcass recovery and post-mortem rates and to transparency with the public on the results of these post-mortems.”
Alan Knight OBE, chairman of British Divers Marine Life Rescue, said: “Even though the salmon farming industry has reduced the seals they shoot over recent years we now need them to take the extra step of employing new techniques to remove the need to shoot any seals at all.”