The Scottish Executive has been asked to examine claims that farmed salmon is unsafe.
Scottish fish farms came out bottom in US study
David Hunter, a consultant to fish farms for 20 years, has warned that the industry is in danger of collapse unless action is taken.
US scientists claimed that the Scottish fish is tainted with chemicals and said people should limit their consumption of farmed salmon.
They have defended their study, which sparked an angry response.
Mr Hunter, of chartered accountants Campbell Dallas, said the executive must act now to secure the reputation and viability of the country's salmon fisheries.
He has called on the executive to fund an independent study into farmed fish.
According to Mr Hunter: "The salmon farmers have been reassured in the past by the Food Standards Agency that their fish is safe.
"But the FSA lacks the credibility to settle this issue and we need a report by a recognised independent authority."
He has also claimed that official backing for the industry fails to match support for farming.
"The industry has been hit by several crises in the past and is expected to weather these storms with neither the financial or political backing shown to industry or agriculture."
The feed used by fish farmers is alleged to contain toxins
The latest threat to Scotland's salmon farms followed a report from researchers at Indiana University.
They claimed to have carried out the most comprehensive analysis to date of salmon toxin concentrations.
The result indicated that farmed salmon from the Scotland and the Faroe Islands had the highest levels of toxins which can cause cancer.
The chemicals are believed to come from concentrated feed used on fish farms.
The research brought a furious response from the industry.
Scottish Quality Salmon, which represents the majority of producers, insisted that the levels of toxins found are well below limits set by the EU and the Food Standards Agency.
And it claimed that the scientists ignored the health benefits of eating farmed salmon.
However, one scientist involved in the research - Dr Jeff Foran of the University of Michigan - said he was confident that the study was accurate.
"All the researchers in the project are top quality scientists and we have worked together collaboratively for the last two years," he said.
"I believe we have developed a scientific study, and we have now published the results of that study, that is definitive."
Deputy Environment Minister Allan Wilson said he felt there was no need for an independent study in response to the American report.
"It provided no new science and the US Environment Agency's contaminant tolerances have been rejected by credible international food safety agencies, including the US Food and Drug Administration," he said.