Pesticides from 12 salmon farms have contaminated lochs around Scotland's coast in breach of safety limits, according to the Scottish Environment Protection Agency (Sepa).

Environmental monitoring by Sepa, the government watchdog, over the last three years has discovered high levels of toxic chemicals in sediments from the Firth of Lorn, the Isle of Lewis, the northwest Highlands and Shetland. Fish farmers use the chemicals to kill the lice that eat away at salmon.

By far the worst pollution was found in Loch Shell on the east of Lewis near a fish farm operated by the Norwegian-owned company, Marine Harvest.

There, levels of a pesticide called teflubenzuron were up to 455 times higher than Sepa's environmental quality standards in 2012.

Sepa is now reviewing the operating licence for the Loch Shell fish farm with a view to imposing restrictions on the volume of pesticides that can be used, and the mass of salmon that can be kept in cages.

In 2011, fishermen blamed pollution from the farm for killing off a valuable prawn fishery in the loch.

Marine Harvest said it was "deeply disappointed" by the pollution detected in Loch Shell. The high levels were "very much outside the norm", according to the company's business support manager, Steve Bracken.

Loch Shell had experienced "a significant challenge" with sea lice, he said, and pesticides had been applied legally and in the correct doses. But he suspected the sophisticated modelling software used to predict their dispersal had failed.

"We need to take action to ensure this does not happen again and we are talking to Sepa about what might work," he said. "One possibility might be to consider alternative locations for the farms.

"We would like to reassure the communities in which we work that this is an unusual occurrence and we continue to carry out our activities in a responsible manner."

Sepa has released the analyses of sediment samples it took from around 24 salmon farms in 2010, 2011 and 2012. It detected residues of pesticides, including teflubenzuron, emamectin and deltamethrin near 19 farms, with only five farms in Orkney recording no contamination above the detectable limit.

Of the 19 with detectable pollution, 12 showed levels of pesticides in breach of Sepa's environmental standards. Four, including Loch Shell, were on the Isle of Lewis, three on the Firth of Lorn around Seil Sound, three in Shetland and two near Kylestrome in the northwest Highlands.

"These sites will be subject to further investigation," said Sepa's fish farming expert, Douglas Sinclair. "The reports enable us to identify the poorest performing operations and direct work and resources to improve any areas of concern."

Guy Linley-Adams, a solicitor who works with the Salmon and Trout Association representing anglers, pointed out that the pesticides were "highly toxic" to lobsters, crabs and prawns. "In the very few lochs where it has looked, Sepa finds plenty of breaches of environmental quality standards," he said.

"The association is left to wonder when, if ever, there will be any sort of robust response by Sepa to stop this happening."

Don Staniford, from the Global Alliance Against Industrial Aquaculture, claimed that "lethal cocktails" of fish farm pesticides were creating "dead zones" in Scottish lochs.

"Chemical use on salmon farms is spiraling out of control as so-called super-lice develop resistance," he warned.

"Lobsters, oysters, crabs and other shellfish are collateral damage in the salmon farming industry's war on sea lice."

According to the Scottish Salmon Producers' Organisation, there were "some anomalies in the reporting" which it planned to discuss with Sepa as soon as possible.

"While the overall picture looks generally encouraging, there is always room for improvement," said the organisation's chief executive, Scott Landsburgh.