Reform is expected for the fishing quotas system which requires fishermen to throw away large amounts of their catch

Ministers from across the EU will take the first steps on Tuesday towards ending the practice of discarding fish at sea, in the most radical change to fisheries policy in 40 years.

At the first high level meeting on the subject, the EU fisheries commissioner, Maria Damanaki, is expected to drive home her message that the current system of fishing quotas must be reformed to spare fishermen the need to throw away large amounts of their catch.

But she is likely to face opposition from some quarters, as member states with large fishing industries jockey for position to try to ensure their fleets enjoy the best deal on quotas.

Richard Benyon, the UK's fisheries minister, said: "The battle lines will be drawn across Europe. We have to change this practice, which is something people rightly find offensive."

The ministers are "working flat out" towards having a reformed common fisheries policy in place by January 2013, according to Benyon, who condemned the current system as "micromanagement from Brussels".

Damanaki told the Guardian this month: "We can't go on like this, with this nightmare of discards.

"We need a new policy."

As much as two-thirds of the fish caught in some areas is thrown back into the water, usually dead, as a result of the current EU system of fishing quotas. When fishing fleets exceed their quota, or unintentionally catch species for which they do not have a quota, they must discard the excess at sea. About 1m tonnes are estimated to be thrown back each year into the North Sea alone.

The waste of edible fish was highlighted in an influential Channel 4 television series, headed by the food writer Hugh Fearnley-Whittingstall, which helped to gather more than 650,000 signatures for a petition to end the practice.

The UK has been working with Scandinavian countries, including Denmark, which has taken a strong stance on the issue, to build up support for reforms to the common fisheries policy.

Benyon said he would propose three alternatives to the current quota system: a "catch" quota, whereby fishermen land all of their catch, monitored by CCTV cameras, but may have the amount of time they can spend at sea curtailed; changes to fishing tackle and techniques to reduce discards; and promoting markets, both within the EU and for export overseas, for fish that are currently little eaten, such as dab and pouting.

"We have tried and tested these solutions, and they work," said Benyon. "We believe they would reduce discards by a huge percentage."

The fishing and food processing industries in the UK support changes that would reduce discards. An unprecedented alliance of retailers and food processors, including Sainsbury's, Marks & Spencer and the UK's Food and Drink Federation, was brought together by the WWF last month to campaign for the reform. They criticised the practice of discards as "the result of poor management and fishing practices that are not attuned to market and consumer needs", and said the common fisheries policy was not working.

The group called on governments to introduce long-term fishery management plans that would include fishermen, giving fleets a bigger role in "co-managing" stocks rather than simply being handed quotas, as under the current system.

Leendert den Hollander, chief executive of Young's Seafood, said: "We welcome the moves to try to tackle discards as we believe the practice is unacceptable – discards are both a waste of resources and a barrier to long-term sustainability in fisheries. We have campaigned against discards for many years and believe that the process of reform must tackled carefully and speeded up because we won't have sustainable fisheries in Europe until all fish caught are landed and properly recorded. Any time wasted will result in more fish being wasted. The way in which we take this responsibility seriously is to encourage consumers to try a wide variety of species."