Scottish ministers have been ordered to name fish farms that shoot seals – and rebuked for trying to keep the hunts secret.

In a damning decision to be published tomorrow, the Scottish Information Commissioner, Rosemary Agnew, rejects SNP ministers' arguments for secrecy as "tenuous". She says she is "disappointed" at the Government's failure to provide evidence in support of its claim that public safety would be put at risk.

Ministers now have to reveal the number of seals killed by fish-farming companies at individual sites before January 10. The only way to avoid doing so is by appealing to the Court of Session on a point of law.

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The Sunday Herald disclosed in September that the Scottish Government was refusing to identify fish farms that shoot seals because of fears that direct action by protestors could put shooters at risk.

This was angrily disputed by anti-fish-farming campaigners, and has now been dismissed by Agnew. "The commissioner accepts that the killing of seals is an emotive subject, and one which could conceivably lead to direct action by protestors," says her ruling. "However, in relation to a potential threat to public safety, the ministers have not provided any specific examples or evidence which would support their view that public safety would, or would be likely to be, threatened."

Ministers referred to protests against a Canadian seal cull, Japanese whaling and a Costa Rican boat cutting fins off sharks, and mentioned demonstrations against a planned seal cull in Orkney more than 30 years ago.

But such examples are "tenuous and bear little relation to the issues or situations under consideration", argues Agnew. "Ministers have failed to demonstrate a real risk or likelihood that the harm they anticipated was likely to occur."

Her decision was welcomed by the Global Alliance Against Industrial Aquaculture, which appealed against the Government's refusal to name the fish farms.

"The public will now be able to avoid buying farmed salmon from farms where seals are killed needlessly," said the alliance's Don Staniford.

Scottish ministers have licensed eight fish-farming firms to shoot more than 300 seals since the start of 2011. Killing them should be a last resort to stop them attacking salmon. But campaigners say it is unnecessary, as seals can be kept out of farms with high-tension nets.

John Robins from the Save Our Seals Fund accused the Scottish Government of siding with fish farms and netters to hide facts from the public. "All we are going to do is compare the number of seals they claim to shoot with eyewitness reports of seal shooting. If these do not match up, the industry and the Scottish Government will have a lot to answer for," he said.

The Scottish Salmon Producers' Organisation (SSPO) accused activists of making "veiled threats".

"We remain concerned about the welfare of individuals who may be identified and targeted by pressure groups," said SSPO chief executive, Scott Landsburgh.

"Farmers are legally required to protect the welfare of their stock and one rogue seal can kill thousands of fish. Removal by anglers, netters and farmers is permitted as a last resort strictly under licence by Government."

The Scottish Government confirmed it had received Agnew's decision. "We are considering its terms," said a spokeswoman.