A new detailed map, developed by the Rivers and Fisheries Trusts of Scotland (RAFTS), identifies the most sensitive locations for the species. The illustration of West Highlands and Hebrides indicates that 57% of the salmon farms in the area are located in the most important areas for wild salmon and sea trout.
Roger Brook, of RAFTS, said: "It is imperative that the salmon farming industry avoids those areas."
He said RAFTS and other wild fisheries groups had argued for years that many fish farms were too close to migratory fish rivers, increasing the risk that sea lice released from fish farms will infect wild salmon and sea trout.
He added that serious consideration should now be given to a selective relocation programme.