ScotS fishermen have given a qualified welcome to the biggest reform in the history of the European Union's fisheries policy.

Measures approved in a vote in Strasbourg include banning discards within three years. This practice of dumping dead fish back in the sea is a result of Common Fisheries Policy (CFP) rules that restrict the size of landed catches under a complex system of quotas.

The package MEPs backed by 502 votes to 137, also has rules to protect endangered stocks.

The day-to-day management of fisheries is to be devolved from Brussels to local levels.

Bargaining over quotas is to be replaced by a move to fishing governed by "maximum sustainable yield" (MSY). This will depend on scientific research into the different species.

But the prospect of an end to discards, which are estimated to represent around 25% of total catches under the present quota system, is especially welcomed.

Campaigners see the move as a vital step to conserving threatened stocks – such as mackerel herring, cod, haddock, plaice and sole – and hope a ban could start later this year. But that is not yet certain.

Since 2001, the total fishing effort by the Scottish fishing fleet has fallen by a massive 69%. But the Scottish Fishermen's Federation (SFF) urged caution over the European vote.

SFF chief executive Bertie Armstrong welcomed the decentralisation of fisheries management. He said: "Rather than a centralised one-size-fits-all policy, we now have a real opportunity to control our fisheries more effectively on a regional basis – where fishermen, government, scientists and other relevant stakeholders can develop effect management regimes. However, there is no indication of the scale of regional control that will be offered.

"As far as discards are concerned, no-one hates discarding more than our fishermen but there is concern about how a ban would work in practice, given the complex mixed fisheries our fishing fleet works in."

Scotland's Fisheries Secretary Richard Lochhead said: "This vote provides a sound basis for discussions with the ministers in the coming weeks. We must not squander this once-in-a-generation opportunity to secure the reform our fishing communities need if we are to ensure that both our marine environment and fishing industry can survive and thrive."

LibDem MEP George Lyon said: "When implemented, these reforms will help end the disgrace of discards. No longer will our fishermen be forced to throw millions of tons of edible fish overboard each year."

Kara Brydson, senior marine policy officer at RSPB Scotland, added: "This is the beginning of the end for overfishing and the wasteful and morally indefensible practice of discards."

Celebrity chef and Fish Fight campaigner Hugh Fearnley-Whittingstall hailed the vote as a fantastic development.

He said: "It's over two years since we launched the Fish Fight campaign, and this is one of the major results we've been campaigning for. We need to keep fighting to make sure the implementation of the ban is rigorous and effective and achieves its principle aim – to eliminate the waste of good fish and help the industry towards a more sustainable future."