Overfishing in EU waters, and the wasteful practice of discarding edible fish at sea, should come to an end from next year, as reforms to the common fisheries policy (CFP) are implemented after seven years of wrangling.

But disputes among member states over rights to dwindling fish stocks mean that key aspects of the plans to improve management of European fisheries are floundering.

From January, the landing obligation should mean that all fish netted are brought to shore instead of thrown away if they exceed a vessel’s quota. By 2020, all stocks should be subject to quotas based on scientific judgments of the maximum sustainable yield, not annual horse-trading among politicians.

EU fishing quotas pose risk to some stocks, say campaigners Read more

However, as fisheries ministers met in Brussels for quota negotiations on Wednesday, it was clear these long-promised reforms would not be implemented in the way campaigners had hoped. Also, there were signs that the UK would face more difficult negotiations after Brexit, as shared waters make up most of the productive seas fished by UK fleets.

The European commission is struggling to insist on the discard ban, against the wishes of some member states. A spokesman said: “The commission has put forward concrete solutions to advance on sustainable fishing and to ease the implementation of the landing obligation, but we cannot do it without the support of the member states.”

While fishing boats have already had their quotas increased to include the quantities that would have been discarded previously, there are “no proper control measures or evidence that the landing obligation provisions are properly enforced”, according to Oceana, an NGO that works on fisheries and the health of the seas.

Facebook Twitter Pinterest Environmental activists protest against fishing policy at the European agriculture and fisheries council in Brussels. Photograph: Olivier Hoslet/EPA

Another problem is the so-called choke species for which there is a low quota, or no quota, but which can be inadvertently taken up when fishing for lucrative species. Once that happens, if a discard ban is in force, vessels must stop fishing. That can be economically devastating for vessels that may not have many days on which they are able to fish.

There are solutions, such as more selective fishing gear and better technology, but the problem could also be solved by swapping quotas among member states or allowing the reallocation of a quotas among vessels within a member state. Yet ministers have been reluctant to explore these.

Rebecca Hubbard of the group Our Fish told the Guardian: “Ministers have been procrastinating and seeking exemptions, including avoiding effective monitoring and control, so unless they are willing to take tough decisions, widespread discarding is likely to continue. This would not only be a waste of a valuable public resource, but a waste of the public’s trust in decision-makers to deliver on the commitments they made in 2013. Ministers could put this right, by setting sustainable limits for all stocks and require electronic monitoring in fleets with a higher risk of discards – it’s worked in north America and Australia, so why not in the EU?”

The CFP reforms, which were first mooted in 2011 and passed in 2013, to be phased in up to 2020, were also supposed to mean an end to the annual bunfights over quotas among member states, in favour of “multiyear management plans”. But while the Baltic and North Sea are now subject to aspects of these plans, the annual quota wrangling is set to continue.

The EU is still technically committed to adopting the maximum sustainable yield – a calculation of how much fish can be taken of each species without harming its ability to recover – from 2020, but that too will be subject to member states’ competing interests.

Key stocks such as seabass, hake, sole and eels are under particular scrutiny. Karmenu Vella, the environment commissioner, has urged ministers to put the long-term interests of fishing fleets before the short-term plundering of stocks, but there has been little sign of his words being heeded.

For the UK, the key deadline is 1 July 2020, by which date negotiations with the EU over new fisheries arrangements are due to finish. For the EU, an essential point of leverage is allowing access to European markets in return for allowing EU fleets to continue to fish in UK waters. Many British fishermen want these issues to be separate, but there is little chance of the government being able to maintain that position.

Without access to EU markets, British vessels – with a highly perishable product that cannot withstand border traffic delays – will lose the export markets that sustain a large proportion of the fleet. Other EU countries have more of a taste for fish, from herring and mackerel to sand eels and scallop,s than British consumers, who tend to stick to a few overfished species such as cod and haddock. The UK imports more fish than it consumes home-caught species.

After Brexit, the commission promises, the UK “will be consulted at various stages of the annual decision-making process in respect of its fishing opportunities”. That means, in effect, a return to the annual quota negotiations, but this time facing off against hostile erstwhile partners who want as much for their own fleets as possible, and who hold a significant advantage if access to their export markets is to be maintained.

Craig Lawson of Oceana said: “Our feelings are that the future fishing negotiations between the EU and the UK will be a nightmare. That is because there are around a hundred shared stocks between the UK and the EU, and negotiations will obviously include access to UK waters and UK vessels in EU waters. Such agreements between multiple parties – the UK will be a third country – make it even more complicated to guarantee the sustainable management of fish.”