More than 5,500 people have signed a Holyrood petition demanding an end to a “Scottish Government-sanctioned seal slaughter”.
Campaigners are urging ministers to stop issuing licences to people they say shoot more than 1,000 animals every year.
They claim most seals are killed by netsmen who fish for wild salmon at the mouths of rivers and by salmon farmers who rear fish in floating factory farms.
The Save Our Seals Fund, which is lobbying the parliament’s public petitions committee, claim salmon farmers could protect their stock by installing predator exclusion nets.
It argues that salmon fishermen should use so-called “acoustic scarers” to keep seals away.
John Robins, of the Save Our Seals Fund, said: “There is a Scottish Government-sanctioned seal slaughter going on based on economics.
“It is cheaper to shoot seals than to humanely keep them away from salmon farms and salmon nets.
“Seals are scapegoats for human greed and this slaughter must stop.
“Apart from killing seals this government policy is damaging the tourist industry, with people cutting their holidays short and going home after witnessing seals being shot.
“We want a total ban on killing seals in Scottish waters.”
But Salmon Producers’ Organisation chief executive Scott Landsburgh said farmers had a duty to protect fish from “harm and unnecessary suffering”.
“They employ a number of deterrents to minimise risk posed by predators,” he added. “It is legal to shoot seals under licence. However, this action is only ever taken as a last resort.”
Highland Conservative MSP Jamie McGrigor said no one supported an unnecessary cull but argued that tens of thousands of seal attacks take place on salmon farms every year.
“The industry maintains that, as a last resort, it needs to shoot persistent rogue seals that attack the nets,” he added.
A Scottish Government spokeswoman said seals were better protected than ever before and shooting was only used as a last resort after “non-lethal alternatives” had failed.
“Our system strikes the balance between protecting seals and supporting our farmed and wild salmon industries,” she added.
“There are no plans to change what is a newly-introduced system.”