The largest study undertaken of pollutants in salmon found chemicals linked to cancer and birth defects present in fish sold by supermarkets and wholesalers.
Levels of 14 toxins were significantly higher in both European and North American farm-raised salmon than in fish caught in the wild. Researchers recommended that only a half to one meal of farmed salmon bought from supermarkets should be eaten per month.
But the most contaminated fish were said to come from farms in Scotland and the Faroe Islands. For these areas, the monthly limit was a mere quarter of a serving.
Wild salmon, on the other hand, could be eaten at levels as high as eight meals per month.
The scientists, from six research centres in the United States and Canada, tracked the source of the pollutants down to the fish meal which is fed to intensively-farmed salmon.
Scottish Quality Salmon (SQS), the industry watchdog, claimed the report was seriously misleading and ignored all the health benefits of regular farmed salmon consumption, as reported in "more than 5,000 scientific studies".
The organisation also argued the study misuses the risk assessment guidelines provided by the US environment protection agency, which they claim are meant to be applied to non-commercially caught fish, and should include consideration of health benefits.
Dr John Webster, a technical consultant for SQS, accused the research of stirring "anti-fish-farming headlines". He pointed out that the report said "individual contaminant concentrations in farmed and wild salmon do not exceed US Food and Drug Administration action or tolerance levels".
Dr Webster said: "PCB and dioxin levels in Scottish salmon are significantly lower than the thresholds set by international watchdogs."
He added that SQS has recently taken steps to maximise the levels of beneficial nutrients in fish, such as omega-3 essential fatty acids, and minimise PCB and dioxin levels by improving processing technology and using high quality fish meals.
The Food Standards Agency (FSA) said the dioxins and PCBs found in the study were within safety levels set by the World Health Organisation and Europe, and urged people to continue eating the fish.
Sir John Krebs, the FSA chairman, said: "Our advice is that people should consume at least two portions of fish a week - one of which should be oily, like salmon. There is good evidence that eating oily fish reduces the risk of death from heart attacks.
"Although dioxin levels have decreased dramatically over the past two decades, we recognise they remain a concern. We advise that the known benefits of eating one portion of oily fish outweigh any possible risks.
"Last year, we asked a group of experts to advise on the risks and benefits of eating more than this regularly over a lifetime. They will report later this year."
But the Green Party leader, Robin Harper, said the findings, published in the journal Science, were devastating and called on the Scottish Executive to launch an immediate inquiry.
"I understand that salmon is regularly assessed by Executive agencies for some pollutants, but this report is a big sign that all is not well and the system of quality control is clearly failing," he said.