Europe’s fish populations will continue to be over-exploited despite a longstanding 2020 deadline for setting fishing quotas at sustainable levels, after ministers from across the EU forced through higher limits than scientists advised.

Key species such as cod in the west of Scotland and Irish Sea, some herring stocks, sole and plaice in the Celtic Sea, pollock in western waters, and ling and tusk in the north-east Atlantic, will all be under renewed and unsustainable pressure, according to campaigners. Quotas for some species were increased from last year, despite advice that they should be brought down.

“The limits agreed by ministers suggest that progress to end overfishing has stalled or even reversed,” said Andrew Clayton of the Pew Charitable Trusts. “This is especially disappointing for 2020, the legal deadline in the common fisheries policy to end overfishing. Missing the deadline means putting stocks such as cod under heavy pressure in 2020, even though their populations are at critical levels.”

The quota for haddock in the North Sea for the UK was raised by 23% and UK catches of sole in the western Channel raised by 19%.

George Eustice, the UK fisheries minister, defended the decisions made at a tense meeting that ended early on Wednesday morning: “This year there has been some very challenging science for cod stocks in many parts of the north-east Atlantic, and we have responded to conserve stocks. I know that some of the quota reductions will be very difficult for some sectors of the industry – however, we know that to protect the profitability of fisheries in the future, we must fish sustainably today.”

He condemned the EU’s “outdated method for sharing quota” among member states, saying it meant the UK got a “very small share of the cod in our own waters”, but pledged that would be reconsidered after Brexit. The UK would also put in place its own policies to ensure fish catches were managed sustainably, he said.

The UK will still have to negotiate with EU member states and non-EU nations such as Norway and Iceland over shared fishing grounds after Brexit.

In an all-night meeting in Brussels, the ministers at the Agriculture and Fisheries Council failed to meet their own targets and deadlines on sustainable fishing, under pressure from their national fleets.

Under reforms to the EU’s common fisheries policy, enacted in 2013 after two years of intense talks, fishing ministers were supposed to gradually phase out the too-high quotas that had been the norm for decades and contributed to steep declines in key fish populations.

By 2020, all quotas were meant to be based on a maximum sustainable yield – the most fish that can be caught without damaging the ability of the species to recover itself – and there was to be an end to the wasteful practice of discarding dead fish at sea.

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But Tuesday night’s meeting, at which the quotas for 2020 were set, showed little departure from the pattern that has been set for years, in which ministers ignored science and fought bitterly for their own vested interests.

“Everybody must comply with the law – and politicians are no exception,” said Andrea Ripol, fisheries policy officer at Seas At Risk. “Ministers decided today to breach the law, allowing overfishing even beyond 2020. This decision represents a betrayal of European citizens, and breaks their trust.”

At the recent UN climate change talks, which ended amid discord and disappointment on Sunday, governments were told that ending overfishing could improve the prospects of dealing with the climate emergency. Protecting fish stocks restores a healthy balance to the seas that enables them to store more carbon and absorb heat, vital functions in the Earth’s natural processes.

“They’re just not getting it,” said Rebecca Hubbard, programme director at Our Fish. “Demonstrating a shocking ignorance of the global biodiversity and climate crisis, the EU council of fisheries ministers refused to follow scientific advice. Ending overfishing would be a rapid, achievable act that would bolster the health of the ocean in the face of the climate crisis, securing futures for coastal communities, as well as being a firm response to calls from EU citizens for climate action.”