Britain’s fishermen will be allowed to increase their catch of cod and other key fish species next year after late-night wrangling between EU ministers in Brussels resulted in a new set of fishing quotas that flout scientific advice.

The quota for cod catches for 2015 will increase by 5% on last year, though scientific advice suggested that it should be cut by 20%.

The UK’s fisheries minister, George Eustice, hailed the deal as a triumph for Britain’s dwindling fishing fleets. He said: “Although these were difficult negotiations, I am pleased that we were able to secure the best possible deal to ensure sustainable fisheries and a strong UK fishing industry. While fishermen had feared there would be major cuts, we were able to keep the same quota as last year for many species, in addition to important increases to the North Sea cod and haddock quota, which will benefit Scottish fishermen.”

UK fishermen will also be allowed to catch 15% more prawns than last year and 15% more plaice in the North Sea, while the haddock catch has been increased by 6%. But in the Celtic Sea, fewer cod and haddock will be allowed to be caught – though the number is still more than scientists advised – and the number of sole to be caught in the Bristol and Eastern channels has been reduced.

Conservationists said the deal, reached after a day and a half of negotiations in Brussels, was not in line with what scientists had advised. After nearly four years of tense negotiations, the EU’s Common Fisheries Policy was finally reformed this year. In its new state, it is supposed to guarantee that fish stocks are managed at what scientists deem to be sustainable levels, known as the maximum sustainable yield.

Andrew Clayton, of the Pew Charitable Trusts, which advocates a sustainable fisheries policy, said: “After decades of failing to get to grips with overfishing, the new common fisheries policy was supposed to bind ministers to setting sustainable fishing limits this year. Instead, they have set a considerable number of [quotas] in excess of the level scientists advised, failing to meet the targets they set themselves for overfishing. These are weak decisions, jeopardising the livelihoods of fishermen and the sustainability of stocks.”

The reforms are supposed to mean that fishing fleets must land all their catch, rather than discarding those specimens or species that are lower value.

Discarding - the wasteful practice of throwing healthy fish back to sea because they are of lower value or because a boat has already reached its quota - has been a particular target of green groups in the last three years, with a campaign spearheaded by the chef Hugh Fearnley-Whittingstall.

However, there are significant gaps in the new regulations that mean many fleets will be able to continue to discard large quantities of fish for several years.

The new European commissioner for the environment, Karmenu Vella, said after the deal was concluded: “We have succeeded in increasing the number of stocks that are now managed at sustainable levels. I can therefore say that sustainably managed stocks are now a broadly accepted concept across the EU. This will allow fishermen to progressively reap more and more benefits in terms of higher catches for these stocks. This is because science-based decision-making is increasingly becoming the norm.”

But he admitted that many of the decisions on quotas were contrary to scientific advice. “We have worked with [ministers] to ensure that where we do not follow science, member states take the necessary decisions to avoid a real disaster happening later.”

Greenpeace EU fisheries policy director Saskia Richartz said: “It is unacceptable that many of the fishing quotas agreed today fail to end overfishing. Ministers gave no justification for postponing action to recover fish stocks, despite new laws requiring that any delay is justified with appropriate evidence.”