The row erupted between St Andrews University and the Scottish Salmon Producers' Organisation (SSPO), the body that represents salmon farmers, over the interpretation of research on the numbers of Atlantic salmon estimated to have been killed by parasites.
It centres on the controversial issue of disease being passed among wild and farmed salmon and it broke out after the research, which salmon farmers say is "wholly incorrect and unjustifiable", was published in the journal Proceedings of the Royal Society B this week.
A press release on an international study involving a St Andrews University professor claimed 39% of salmon deaths in the Atlantic were due to sea lice, but the salmon farmers claim this figure is calculated at between 1% to 2%.
The university last night said it "stands by its research and press release".
Professor Phil Thomas, chairman of the SSPO, has written to Professor Louise Richardson, principal and vice-chancellor asking for an apology and an independent inquiry.
He claimed: "The effects of sea lice on the ocean mortality of wild salmon are very small, representing about 1% to 2%, rather than the 39% that was claimed in the media statement. This is consistent in both the previous scientific studies and their data.
"To make these wholly incorrect and unjustifiable claims damages both the scientific reputation of the individuals concerned and the institution.
"I am entirely at a loss to understand how a reputable university like St Andrews can have become embroiled in a process of public misinformation of this type."
In the press release, the university said an "unexpectedly large" number of free-ranging salmon are being killed by parasitic lice in European waters every year.
Professor Christopher Todd, of the Scottish Oceans Institute at St Andrews, was part of an international group involved in the study.
He said in the release: "The salmon aquaculture industry has long placed a high priority on controlling sea lice on their captive salmon – but these results do emphasise the need for the industry to not only maintain the health of their own stocks, but also to minimise the risk of cross-infection of wild fish."
Mr Thomas said: "The paper does not make any evaluation of the impact of salmon farms on wild salmon losses, although it attempts to make an opinion link to salmon farming."
A spokesman for the university said: "We stand by our part in this research, which was published in Proceedings of the Royal Society B, and we stand by our press release, which was agreed by all three authors.
"The central, unequivocal finding of this research paper, as presented in our press release, is that parasites such as sea lice are responsible for an average of 39% of all salmon deaths at sea.
"We reject Professor Thomas's substantial and unwarranted comments on the University of St Andrews."