The Sea Shepherd Conservation Society says the Scottish Government's new system of issuing licences to shoot seals, which will allow more than 1000 to be killed this year, is simply a charade for the benefit of badly managed fish farms and sporting estates.
Although the mammals sustain many tourist businesses, they are seen as a risk to fish farms and wild fishery interests. Environment Secretary Richard Lochhead has said controls on the number of seals that can be shot strike the "right balance" between seal conservation and support for fisheries and the fish farming industry.
However, David Scott, a UK Trustee for Sea Shepherd, has criticised the decision to set limits on the number of seals that can be shot and contrasted the situation with ministers' refusal to ever use existing powers to allow the killing of some birds of prey by sporting estates.
He said: "It is interesting to note the obvious discrepancy between the Government's refusal to permit raptor killing licences for game bird estates while permitting seal killing licences for the water features on those same estates."
The Scottish Government has said that, after the new measures were introduced last year, under the Marine (Scotland) Act 2010, 362 seals were shot in the first three quarters of the year, just 27% of the maximum allowed under licence.
Now the maximum number that can be shot has been reduced by 15% this year from 1340 in 2011 to 1100 this year.
But Mr Scott said the numbers shot were now far higher than before the legislation was introduced and he questioned claims that this was an improvement.
Mr Scott said: "During 2008, 2009 and 2010, Marine Scotland reported approximately 80 seals shot in total.
"In the first nine months of the act they have trebled the kill count. So we remain baffled as to how issuing licences to shoot more seals than the highest Government estimate of illegal killing represents some kind of improvement. It doesn't. It isn't.
"The seal licence project could therefore be considered simply a charade to ensure seal killings are now legally permissible for the benefit of the worst-managed fish farms and the most arrogantly managed hunting, shooting, fishing estates."
Mr Scott also said none of these businesses would have any incentive to clean up their act until the Government introduces a zero-kill policy.
But a Scottish Government spokesman said: "The 2010 Marine Act provides an unprecedented level of protection for Scottish seals and – for the first time – it is now illegal to shoot a seal except under very strict licensing conditions. This has meant far fewer seals are being shot than in the past.
"The vast majority of seals head to feeding grounds at sea, however a few individuals repeatedly target migrating fish, entering freshwater river fisheries and coastal nets, or attack stocks in fish farms."
These seals could be shot as a last resort, the spokesman added.
Scott Landsburgh, chief executive of Scottish Salmon Producers' Organisation, said: "We have a moral and ethical responsibility to protect our fish. We also have a legal responsibility under current animal welfare legislation to give full protection to our fish against persistent aggressive predators."