Nature is infamously red in tooth and claw but the sustained battle between Scotland's salmon farmers and anglers who fish for the wild variety rivals any conflict in the natural world.

The conflict has resumed with a complaint to the European Commission that the district salmon fishery boards, which control fishing on Scottish rivers, and the Scottish Government are failing to comply with a European directive on conservation. The complaint by Dr Martin Jaffa, made through his fish-farming consultancy Callander McDowell, calls for an end to recreational angling of spring salmon to help preserve declining stocks.

The timing, as MSPs on the Rural Affairs Committee prepare to hear evidence on the Aquaculture and Fisheries Bill from freshwater fisheries, is a further ratcheting up of tension between the fish-farming interests and the angling lobby.

The purpose of the Bill, according to the Scottish Government, is to ensure farmed and wild fisheries – and their interactions with each other – continue to be managed effectively, maximising their combined contribution to supporting sustainable economic growth with due regard to the wider marine environment. Illustrating just how contentious this is, the legislation has given new focus to the increasingly bitter dispute between the fish-farming industry and wild fisheries.

It is more complex than protection of the environment and conservation of species versus sustaining a significant contributor to the Scottish economy. The economic importance of the fish-farming industry's £540 million in exports is obvious. Farmed salmon is now Scotland's biggest food export, while salmon and sea trout angling contribute about £100m to the rural and tourism economy.

Dr Jaffa's complaint that district salmon fishery boards are failing in conservation responsibilities is a response to the angling lobby's accusation that the salmon farming industry takes a reckless attitude to the environment. Freshwater fisheries have blamed sea lice from fish farms for killing wild salmon and threatening to devastate fish stocks in Scottish rivers. Dr Jaffa says the boards should have restricted catches of spring salmon and calls for the angling season to be shortened and 100% catch-and-release to be imposed until stocks recover.

By using figures showing 46,000 spring salmon caught and killed from 11 conservation area rivers since 1992, he ignores the increase in catch-and-release in recent years. Last year, 70% of rod-caught salmon and grilse in Scotland were put back, including 91% of spring salmon, and the figures indicate stocks may be stabilising.

The Fisheries Bill has alarmed the fish-farming industry with proposals that would give officials greater powers of inspection on salmon farms and require them to comply with stricter codes of practice involving control of sea lice.

Neither side of Scotland's farming industry can claim to have followed best environmental practice. Instead of recrimination they should recognise that conservation and environmental responsibility are in the interests of both.