A row erupted after St Andrews University claimed 39% of Atlantic salmon deaths were due to parasites, while salmon farmers, represented by the Scottish Salmon Producers Organisation (SSPO), said the figure is 1% to 2%.
Both sides extrapolated their conclusions from near-identical data. The SSPO accused Scotland's oldest university of misleading the nation. St Andrews is standing by its findings.
While it has been claimed sea lice thrive among farmed salmon kept in coastal cages, the Government said that the case was not proven.
A Scottish Government spokesman gave no explanation for the reasons for such a wide variation in conclusions.
He added: "We will consider carefully the recent St Andrew's University report on the impact of sea lice on wild salmon in the marine environment.
"The study acknowledges it does not provide any new data on the impact of sea lice on salmon, nor was it about the particular effects of fish farms, but rather brings together data from a number of studies in Norway and Ireland and analyses them in a new way.
"We recognise there are disagreements between the parties over the interpretation of the report.
"The Scottish Government continues to consider any evidence of an impact on wild fish stocks from fish farms, but the suggestion that the decline of wild salmon stocks in Scotland is as a result of sea lice emanating from fish farms is not proven.
"It is, however, appropriate that interested parties continue to discuss and debate the evidence and we would encourage them to do so in a constructive way."