Fisheries ministers meeting in Brussels to decide EU quotas for next year have set some stocks within levels scientists deem sustainable but left many others vulnerable to overfishing.

The ministers also said there would be a review of the planned ban on the discarding of edible fish at sea, which could, in effect, mean the wasteful practice is allowed to continue despite an eight-year battle to end it.

For the UK, there were substantial increases in quota for a few species, including monkfish off western Scotland, which was up by a quarter, western hake, which was increased by more than a quarter, and a 10% increase in fishing for skates and rays in the Channel.

George Eustice, the fisheries minister, said: “We entered into discussions knowing that a good deal needed to carefully balance progress towards sustainability targets, while ensuring that we listen to the scientific evidence on the health of fish stocks and safeguard a profitable future for our hardworking fleet.”

Next year is a crunch point for EU fisheries policy because an overhaul worked on since 2011, and passed in 2013, requires that by 2020 all fishing quotas must be set within scientific advice, known as the maximum sustainable yield, meaning the amount of fish that can be taken without harming species’ ability to recover.

This year’s meeting, which ended in the early hours of Wednesday morning, suggests there is little chance of those aims being achieved, according to campaigners.

Jenni Grossmann, a senior policy adviser at the environmental law charity ClientEarth, said: “EU ministers have once again signed off overfishing for certain stocks in European waters, including vulnerable species such as whiting in the Irish Sea and cod in the west of Scotland and the Celtic Sea.

“This year’s negotiations were the penultimate chance for ministers to get on track to meeting the 2020 legal deadline for sustainable fishing limits. By disregarding scientific advice, they are delaying stock recovery and risking even more painful quota cuts next year.”

Scientific advice on the maximum sustainable yield was followed for 59 stocks, but there are more than 100 governed by the quota system; in the north Atlantic, advice was mostly not followed, according to campaigners. More than half of the North Sea and north Atlantic key stocks have been estimated to be overfished.

Rebecca Hubbard, the programme director at Our Fish, a campaigning organisation, said: “This should have been the year in which fishing quotas finally followed scientific advice, and EU fisheries ministers made history by ending overfishing in EU waters.

“Instead, we saw another absurd all-night meeting behind closed doors, where ministers haggled over fishing quotas like kids trading football cards. By choosing to set fishing limits above scientific advice for many stocks, they have ignored European citizens and all of the evidence that shows ending overfishing will deliver healthy fish stocks, more jobs and security for coastal communities.”

The discard ban would also not live up to the promises made by the European commission over the past eight years, Hubbard said. “Fisheries ministers have been procrastinating and seeking exemptions to the ban on discards, including avoiding effective monitoring and control. As a result, widespread discarding is likely to continue in 2019,” she said.

“This is not only a waste of a valuable public resource, it is a waste of the public’s trust in decision-makers to deliver on their commitments. Ministers could have put this right today, by at least requiring cameras on boats with a higher risk of discards – it is what they are doing in North America and Australia – but they have kept their heads in the sand with less than 2% monitoring at sea instead.”

This year’s decisions have been overshadowed by Brexit. Other EU member states were reluctant to have their quotas cut when the UK may face difficult negotiations with the bloc next year.

Although in theory the UK could win back more fishing rights after leaving the EU, in practice this will be hard to achieve, because other member states are likely to drive a hard bargain, particularly over allowing access for UK fish exports to the vital EU market, and because the government has signalled it does not plan big changes to the way the industry is run and quotas allocated.

Scotland’s cabinet secretary for rural economy, Fergus Ewing, said the final deal was disappointing for fishermen in some outcomes, with reduced quota limits for some stocks.

“It is worth noting that we were not in isolation, with reduced quotas being faced by all member states across the board,” he said. “We had always suspected that this would be a particularly difficult council, and so it proved to be.”

Mike Park, the chief executive of the Scottish White Fish Producers Association, said: “The dynamics of negotiations this year were always going to be complicated, given full introduction of the landings obligation [discards ban] and the fact this is our last fisheries council as a fully-fledged member state.

“The outcome is less than we hoped but as much as was possible under the circumstances. The important outcome is that our fleets should now be able to fully utilise the opportunities available to them in 2019.”