110 seals have been shot so far this year to protect the salmon industry, an ITV News investigation has found.
Although they are officially protected, seals can be shot under a special licence.
Salmon farmers and fishermen are allowed to shoot seals attacking their stock.
Campaigners say non-lethal means should be used to deter marine mammals.
Philip Mansbridge, UK Director of the International Fund for Animal Welfare (IFAW), has said "it will be shocking to many people to learn" that despite seals having protected status they can still be shot under licence to protect the salmon industry.
New figures from the Scottish government have revealed that 110 seals have been shot so far this year.
Because shooting is permitted all year round dependent pups are left to starve if their mothers are shot, says charity.
The RSPCA has outlined in detail its policy on the shooting of seals that attack salmon stocks "as an absolute last resort".
The RSPCA is being criticised over its new welfare standards which permit salmon farmers to kill seals that attack fish stocks.