The international study involving the University of St Andrews said the parasite was responsible for an average of 39% of all salmon deaths at sea.
Angling groups claimed this confirmed the impact of fish farms on salmon.
The Scottish Salmon Producers’ Organisation (SSPO) and St Andrews have now clashed over the results.
The SSPO has written to the university demanding a retraction of the press release issued to publicise the research, and also an apology.
The organisation said ocean mortality of salmon was widely recognised to be at more than 95%, with sea lice representing 1-2% of deaths according to previous scientific studies.
It added that declines in numbers of wild salmon to Scottish rivers to spawn had affected the east coast, where there are no salmon farms, as well as other parts of the country.
Prof Phil Thomas, chairman of SSPO, accused the university of making “a major blunder”.
The University of St Andrews said it stood by its part in the research and its press release.
“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.”
Ten others were refloated after being kept alive by vets from British Divers and Marine Life Rescue.
The whales which survived will be monitored for the next 24 hours to see if they re-beach.
Three of the whales which died were calves.
The incident drew a large number of bystanders to the scene, prompting the coastguard to urge the public to stay away to allow rescue teams to carry out their duties.
A further 24 pilot whales, thought to be from the same pod, were spotted in shallow water about three miles away at Cellardyke.
They have been monitored for signs that they are in danger of stranding.