FISHERMEN and fish farmers have urged the Scottish Government to rethink strict limits on the number of seals which can be shot this year.

After measures were introduced last year to protect seal populations, the number of animals killed fell from 3000 a year to just 362 in the first nine months of 2011.

Environment Secretary Richard Lochhead said yesterday the indications were the first year of controls had worked well to protect an iconic species and this year the Government will allow less than 1% of Scotland's seal population – a maximum of 1100 seals – to be shot.

Ministers say measures are in place to control the removal of seals around fisheries and fish farm cages as a last resort, but industry officials have criticised the decision to reduce the number of seals which can be culled by 15% this year.

They also pointed to figures which show growing numbers of seals in Scotland and the impact of grey seals on the fish population – they are estimated to eat around 200,000 tonnes of fish every year in Scotland.

Ken Coull, fisheries policy officer at the Scottish Fishermen's Federation, said: "In their most recent advice for cod on the West of Scotland, the International Council for the Exploration of the Seas acknowledged the contribution of seal predation to total catch mortality is likely to be significant.

"If these figures are correct, this will have every bit as much an impact as our restricted fishing efforts. What is the net gain of putting controls on fishing,  when unaccounted mortality, including seals, has three or four times the impact on stocks?"

Scott Landsburgh, chief executive of the Scottish Salmon Producers' Organisation, said the official Scottish Government figures are in line with previous reports by the industry and demonstrated "the commitment to shoot as a last resort only, whilst balancing conservation with sustainable aquaculture and wild fisheries".  But he added: "Official figures from the Special Committee on Seals suggest there are over 128,000 seals in Scotland, so the proposal to reduce the permitted maximum amount under licence is premature."  

It was estimated 3000 seals were shot each year before the new measures came in last year. In the first three quarters of 2011, 362 seals were shot, just 27% of the permitted maximum under licence of 1340. Ministers have reduced that by 15% this year to a maximum of 1100 seals.

Mr Lochhead said Scotland's seals were an iconic species and through the Marine Act 2010 a raft of new measures had given extra protection, including the creation of conservation areas.

He said: "I'm pleased the right balance between seal conservation and support for important wild fisheries and our fish farming industry is being struck."

But John Robins, campaigns consultant to Animal Concern and secretary of the charity Save Our Seals Fund, said: "The shootings take place in remote areas with no witnesses to verify the numbers shot. The Government relies on figures submitted by the shooters themselves to collate figures."

He called for salmon farmers to be legally required to install and maintain anti-predator nets to exclude seals from their farms. Fish farmers, however, say anti-seal measures are already taken but algae can grow on extra netting, reducing oxygen flow to the fish.