The European parliament voted on Wednesday to ban the wasteful practice of throwing away healthy fish at sea in a victory for campaigners and green groups after more than two years of procedural wrangling.

Campaigners in Strasbourg for the "historic" vote on the EU common fisheries policy (CFP) were jubilant. After significant opposition to the changes from the powerful industrial fishing lobby, and multiple attempts to scupper the process, the final vote was won by an emphatic 502 votes to 137.

"This is really excellent news," said Hugh Fearnley-Whittingstall, the chef and food writer who spearheaded the Fish Fight campaign that mobilised hundreds of thousands of people to oppose discards. "It was a nerve-racking morning – there was still a faction who wanted to derail the process – but well done to the MEPs, and well done to the Fish Fighters."

Discarding – where fishermen toss back hundreds of tonnes of edible fish, usually dead, because they have exceeded their fishing quota or have caught species for which they have no quota – has been the most striking example of the failures of a common fisheries policy that green groups have said is "broken" and encourages overfishing instead of protecting dwindling stocks. Between one-quarter and one-third of the total catch quota is estimated to be discarded, and this may rise as high as 90% of the catch in some circumstances for some species, according to Fish Fight.

The vote makes it highly likely that the biggest shake-up of the common fisheries policy for decades will pass into law, perhaps next year. It is still not quite final, as there must be some further negotiations with member states, but campaigners said the reform proposals were now over the biggest hurdles to their adoption.

"The MEPs have sent a really strong, clear message – it would be very difficult for member states' ministers to try to go against that," said Fearnley-Whittingstall.

Maria Damanaki, the EU fisheries chief, who brought forward the proposals, welcomed the vote. "[This policy] introduces a discard ban with clear dates to put an end to wasteful practices that we can no longer afford. I am looking forward to the work that the council and the parliament will soon start to ensure the adoption of the reform of the CFP."

Sections of the EU's fishing lobby, particularly in Spain and France, have opposed the changes. Many operators of large industrial-size vessels would prefer to continue to be allowed to discard healthy fish – if they in particular are forced to land all the fish they net, they could end up with catches of lower value species, or lower quality specimens, so being able to select the highest value fish can help them maximise their profits.

Last year, member state ministers passed the reforms after an all-night negotiating session, but it is possible that the fishing lobby will make a last-ditch attempt to have member states derail or water the changes down in the final stages of the process. But Saskia Richartz, EU fisheries policy director at Greenpeace, said: "This vote signals a momentous shift away from overfishing and is a testament to parliament's resolve to defend the general interest. National governments that stand in the way of reform, like Spain and France, will find it increasingly hard to act as proxies for a handful of powerful companies, with no concern for the long-term wellbeing of the oceans or the majority of fishermen."

The changes would also put an end to the annual wrangling over fishing quotas, which campaigners say leads to overfishing rather than protecting stocks. In future quotas would be based on longer term "maximum sustainable yield", set taking scientific advice into consideration.

Barrie Deas, chief executive of the UK's National Federation of Fishermen's Organisations (NFFO), said he welcomed the vote, but said the reforms could be hard to put into practice. "The history of the CFP has been littered with well intentioned pieces of legislation that have failed because insufficient attention had been paid to how the measures could be implemented. There is good and bad in the compromise text. [On discards] the real issue concerns the practical issues of applying such a policy at the level of each individual fishery."

Greenpeace has accused NFFO of being dominated by the interests of large industrial fishing companies, many from overseas.