Members of Holyrood's Rural Affairs Committee said the adversarial dealings between the two parts of the industry had hindered their scrutiny of new legislation.
They said improving the relationship between the two sectors was "perhaps of equal significance for Scotland in the long-term" as changing the law.
The Scottish Government has put forward a Bill that aims to reform the management of the fish farming and wild fisheries sectors.
Committee convener Rob Gibson said both were of critical importance to Scotland, but added: "These sectors are clearly at loggerheads over a number of issues, which has hindered our scrutiny of this Bill."
The two sectors were recently embroiled in a row over a controversial report released by the University of St Andrews, which claimed 39% of salmon deaths in the Atlantic were caused by sea lice, a parasite often associated with farmed salmon. However, salmon farmers fought back by saying the real figure of the effect of sea lice on the ocean mortality of wild salmon was only 1% to 2%.
Members of the committee backed the general principles of the Aquaculture and Fisheries (Scotland) Bill, but also argued it needed to be more robust.
MSPs visited salmon rivers, wild fisheries hatcheries, fish farms and processing plants to build up a detailed understanding of the industry.
However, their report said their work was "hindered by some of the more adversarial, tit-for-tat engagement of sections of both the aquaculture and wild fisheries sectors".
The MSPs said: "As important as this legislation is, perhaps of equal significance for Scotland in the long-term is improving the current relationship between the wild and farmed fishing sectors, with a view to establishing closer, productive, co-operative working relationships."
In response to the comments, Scott Landsburgh, chief executive of the Scottish Salmon Producers' Organisation (SSPO), said: "We share the committee's views that angling interests and salmon farming are both important to the Scottish economy and intend that the current regular dialogue with angling representatives – and the examples up and down the west coast of very positive, local relationships between both groups – will underpin greater mutual understanding and a successful future for both industries."
The Salmon and Trout Association, the Association of Scottish Shellfish Growers and the Scottish Anglers National Association were also approached by The Herald but were unavailable for comment.