A report by the Worldwide Fund for Nature (WWF) and the Atlantic Salmon Federation says too little is being done to prevent salmon farms from causing environmental damage.
Salmon farming in the sea lochs of Scotland has expanded to become a major industry.
The report says the decline in stocks is linked to sea lice from farmed salmon sites, and interbreeding between escaped fish and the wild population.
As the number of farmed salmon has exploded, the population of its wild relatives has crashed.
Stormy waters
Estimates suggest there are 48 caged salmon to every wild one in the North Atlantic.
The link between the increase in farmed salmon and the decline in the wild population is hotly disputed, although recent research suggests salmon farms have spread disease.
Friday's report claims that the Scottish authorities, and those in other countries, have failed to live up to international commitments to protect wild salmon.
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We need the aquaculture industry to be managed better so we don't see the demise of salmon
"
WWF Scotland's Helen McLachlan
It says measures like locating farms away from the mouths of rivers where migrating fish are most likely to be harmed have not been implemented.
WWF Scotland's Helen McLachlan said it was "extremely concerned" at the decline in the wild salmon population.
She said: "This is a species that we don't want to see lost and aquaculture has a significant impact on those populations.
"We need the aquaculture industry to be managed better so we don't see the demise of salmon."
Policy review
The Scottish Executive said it had recently published a plan to create a better balance between the interests of wild and farmed salmon.
But the environmental groups say it has to deliver results quickly if salmon is to survive in UK seas and rivers.
In March, Deputy Environment Minister Allan Wilson said £100,000 would be set aside annually to support the establishment of a Scottish Aquaculture Research Forum.
He also promised a review of policies on the situation or relocation of fish farms in coastal areas.
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