The Scottish Government allowed a US drug company to secretly rubbish a scientific study blaming one of its pesticides for killing wildlife in Scottish sea lochs.

The Sunday Herald has uncovered that the £76 billion New Jersey multinational, Merck, hired reviewers to criticise evidence in a scientific study that the company’s fish farm chemical was causing widespread environmental damage.

The scientists behind the study and the Scottish Environment Protection Agency (Sepa) privately protested about Merck’s involvement. But they were overruled by government and salmon industry officials who insisted that the company’s role should be kept secret.

Merck’s behind-the-scenes influence has been exposed by more than 70 megabytes of internal documents released by the Crown Estate under freedom of information law. They also show that government and industry agreed not to issue a press release on the study.

The revelations have been described as “extraordinary” by environmentalists, who are demanding a ban on the pesticide. Merck said that the study had “limitations” and the Scottish Government defended the anonymity of reviewers.

Merck, known as MSD Animal Health in the UK, makes Slice, a pesticide containing emamectin benzoate to kill the sea lice that plague caged salmon. The Sunday Herald disclosed in February that at least 45 lochs were contaminated with the chemical.

We subsequently reported that Sepa had suppressed a report about emamectin and ditched a plan to ban it after pressure from the fish farming industry. But until now the role of Merck has remained hidden.

Central to the saga is a study carried out by the Scottish Association for Marine Science (SAMS) in Oban for the Scottish Aquaculture Research Forum (SARF). SARF is a charity funded by the Scottish Government and the fish farming industry to support a “sustainable” fish farming industry.

The study, which was posted online in August 2016, suggested that emamectin contamination of the seabed was causing “substantial, wide-scale reductions” in crabs, lobsters and other crustaceans. But it was contained within a second report that cast major doubts on its findings.

The second report was said to have been the result of concerns from “independent” but unnamed referees. But internal communications name Merck as responsible for the criticisms.

In a 25-page response to the criticisms in December 2015 Professor Kenny Black and Dr Tom Wilding from SAMS said that four of the five reviewers were “from Merck”. In an email to SARF in May 2016 they warned that “questions will be asked about the independence of the review process”.

In another email the following month they expressed concern that refusing to admit the company’s role “might reflect negatively” on the review “if/when this information becomes public.”

Their concerns were supported by Sepa’s fish farming expert, Douglas Sinclair, who described the criticisms from Merck’s referees as “rather harsh”. However he added that Sepa would not make “an issue” of the matter given it was likely to be a “lone voice” late in the process.

Other emails show officials from the Scottish Government, the Crown Estate and the fish farming industry on SARF’s board of trustees all agreed that the identity of referees should remain confidential. They also decided not to press release the study.

The documents were obtained by the wild fish campaign group, Salmon and Trout Conservation Scotland. “This is a classic of how to deal with the unwanted results of environmental research,” said the group’s lawyer, Guy Linley-Adams.

“Allow those most threatened by the research to organise and hold sway over a peer review process, ensure that reviewers are set up to review extremely critically, give them anonymity. And then try to bury the report for good measure.”

Linley-Adams described Sepa’s failure to stand up to the process as “shocking” and demanded that it bans emamectin. He accused the Scottish Government of going “along for the ride with the fish farming lobby”.

Dr Richard Luxmoore, senior nature conservation adviser at the National Trust for Scotland, said: “It is extraordinary that SARF could think it acceptable to use consultants employed by the manufacturers of the chemicals to review a report on their environmental impact.”

He added: “The efforts that these reviews have made to pick holes in a study of environmental pollution are remarkable. They read not like objective evaluations, but more like a concerted attempt to discredit an inconvenient truth.”

The Scottish Creel Fishermen's Federation has labelled pollution from fish farms as “the biggest darkness on our doorstep”. The federation’s national coordinator, Alistair Sinclair, accused the government of “playing fast and loose with the marine environment”.

Merck’s UK arm, MSD Animal Health, stressed the value of emamectin in controlling sea lice, and its support for high quality research. “We have noted some limitations in the retrospective analysis purporting to assess the effects of emamectin benzoate on benthic crustaceans,” said a company spokeswoman.

Emamectin had been approved by regulatory agencies in all countries where sea lice were a significant problem for the salmon industry, she added. “It has been used for more than 15 years for the safe and effective treatment and prevention of infestations of all parasitic stages of sea lice on Atlantic salmon.”

The Scottish Government highlighted its commitment to “sustainable growth” of the fish farming industry. “It is normal for the reviewers of scientific work to be anonymous and several reviewers are used to make that process robust,” said a spokesman.

According to the fish farming industry, the SAMS study was inconclusive. “The board of SARF felt that it was important for a layman's commentary to be published alongside the report to explain their reservations and set its findings in proper context,” said Scott Landsburgh, chief executive the Scottish Salmon Producers’ Organisation.

SAMS said it stood by its study, adding that it reported its results “openly and without prejudice.” Sepa pointed out that the experts involved in peer reviews were not always named.

The Crown Estate just said that the report had been published. SARF did not respond to requests to comment.