A last-ditch attempt by Scottish ministers to keep secret the identities of salmon farms that shoot seals has been rejected by Scotland's freedom of information watchdog, Rosemary Agnew.

The Sunday Herald can reveal that she has ordered the Government to name the individual fish farms by May 7. The argument that identifying the farms would put those shooting the seals at increased risk of attacks by animal-rights campaigners was not "compelling", she concluded.

Agnew's decision has been welcomed by environmental and animal-welfare groups, but attacked by the fish-farming industry. The Scottish Government said it was "disappointed" with the decision but would have to comply.

According to official figures, fish farmers shot 449 seals in 2011 and 2012 to prevent them from eating salmon. A further 443 seals were killed around the coast by salmon netting firms and river fisheries.

The Scottish Government last year refused to name the specific fish farms responsible for the shootings, claiming that shooters could be put at risk of direct action by protesters. In December, its arguments were dismissed as "tenuous" by Agnew, the Scottish Information Commissioner.

But in an unprecedented move in January, she reopened her investigation due to new evidence from salmon-netting companies. They claimed to have received threats from animal-welfare groups, including a death threat.

Now, however, Agnew has concluded that the evidence was not enough to deter her from enforcing her original decision.

She said: "The evidence does not provide a compelling argument that the threats are any more likely to occur or be acted upon because of the information being disclosed."

She added: "Retrospective information is unlikely to provide sufficient detail for threats to be the result of targeted action."

And she pointed out those who had made threats in the past were aware who shot seals and where.

The names of the fish farms licensed to shoot seals were requested by Don Staniford, from pressure group the Global Alliance Against Industrial Aquaculture.

He said that Agnew should be applauded for rejecting "government censorship". He called on fish farmers to stop shooting seals, and instead install anti-predator nets.

According to the Scottish Government, only one in five of Scotland's 215 active fish farms have predator nets. The government has not insisted on the nets because they can trap and kill other animals, such as otters and dolphins.

Libby Anderson, the policy director of the animal-welfare group, OneKind, said: "Public concern about the extent and nature of seal shooting is both justified and legitimate, and Scottish ministers have not advanced any evidence to convince the commissioner of a real risk to public safety if this information is released."

But Scott Landsburgh, chief executive of the Scottish Salmon Producers' Organisation, said: "Clearly, satisfying campaigners and achieving headlines is more important than public safety.

"We stand with salmon netters in our commitment to exclude and deter seals and to shoot only when all other measures fail. This is entirely legal and necessary to protect fish welfare."

The Scottish Government reiterated the "potential risk to public safety" from naming fish farms.

A spokeswoman said: "That risk is something that has now been acknowledged by the Scottish Information Commissioner, even though her final decision is to enforce the release of the information."