The SNP administration says it fears direct action by animal-rights protesters trying to save seals could put the lives of the marksmen at risk.
This claim has been dismissed as "blatant scaremongering" and a "ludicrous excuse" for official secrecy by animal welfare campaigners. They say they would act within the law, and would not do anything that would endanger fish-farm workers.
Scottish ministers have licensed eight fish-farm companies to shoot more than 300 seals since the start of 2011. Killing is meant to be a last resort to prevent them from eating salmon from underwater cages.
But the killing has faced fierce opposition from campaigners, who argue it is cruel and unnecessary. Instead, seals can be stopped from taking fish by high-tension nets, they say.
In response to freedom of information requests, the Scottish Government has released figures showing which fish-farming companies have shot the most seals. But it has refused to name the individual farms where the shooting has taken place.
Campaigners have appealed to the Scottish Information Commissioner, Rosemary Agnew, who has begun to investigate. In a submission to Agnew last month, the Scottish Government said there was a "strong likelihood" campaigners would take direct action "against individuals employed at sites where seals have been shot".
David Scott from Sea Shepherd UK – an ocean conservation organisation – told the Sunday Herald: "I would willingly put myself between a government-licensed killer and his intended victim, especially if that was a pregnant or nursing seal. I would do no harm to the rifleman, nor would I break any laws in doing so – but I would protect the seal."
The Government has also claimed that at a meeting with Environment Minister Richard Lochhead, Sea Shepherd's Scott made a "scarcely veiled threat" to prevent seal shooting. He provided "no specific details of what kind of action he had in mind, possibly for tactical reasons," it alleged.
The Government's submission added: "In the past, fringe animal-rights groups have targeted individuals implicated either directly or indirectly in shooting seals with verbal abuse, hate mail, unpleasant and noxious parcels, physical intimidation and even assault, and have also caused property damage."
But Scott told the Sunday Herald: "This is blatant scaremongering with zero corroborative evidence and is a gross insult to an organisation which has never harmed a single person in its entire 35-year history."
"No representative of Sea Shepherd would ever permit harm to any person, no matter how vile their actions. Sea Shepherd always seeks to take preventive action within the law to protect marine wildlife." Scott added he made "no veiled threats whatsoever".
Sea Shepherd is a radical conservation organisation, famous for using its boats to try to stop Japanese whalers. Its leader and founder, Paul Watson, is currently on the international police wanted list after he skipped bail in Germany in July to avoid what he said were "bogus" charges by Japan.
Don Staniford from the Global Alliance Against Industrial Aquaculture called for all salmon farms guilty of shooting seals to be named and shamed. "The Scottish Government should be ashamed of itself for shielding Scotland's foreign-owned salmon farms from public scrutiny," he said.
John Robins, secretary of the Save Our Seals Fund, said the public had a right to know seal-shooting sites so numbers could be checked.
The Scottish Government confirmed it did not "routinely" disclose the sites issued with seal-shooting licences. "This is due to the risks of individual fisheries or fish farms, or their employees, being identified and becoming the target of action by interest groups," said a government spokesman.
The Scottish Salmon Producers' Organisation pointed out there are more than 120,000 seals in Scotland. Millions of pounds were invested in non-lethal ways of keeping them away from fish farms, it said, and fewer than half of those shot were at farms, with the rest killed by anglers and netters.
"Farmers are legally required to protect the welfare of their salmon," added the organisation's spokesman. "As one rogue seal can kill thousands of fish, removal by anglers, netsmen and farmers is permitted as a last resort strictly under licence by the Scottish Government."