The European parliament has voted on a series of measures likely to reduce overfishing in the North Sea which will affect the UK’s fishing fleet until Brexit takes effect and potentially beyond.

The vote ensures that there will be limits to fishing quotas so that they cannot exceed levels regarded as sustainable by scientists. The outcome had been in doubt as MEPs voted on Thursday, but several amendments aimed at watering down the proposals were rejected.

The North Sea is one of Europe’s biggest fishing grounds, especially for key commercial species such as cod and haddock. But the UK has threatened to withdraw from the EU common fisheries policy (CFP) as part of Brexit, which would throw the future of fishing stocks in the area into doubt. The proposals will now be finalised by member states.

Even after Brexit, the UK will have a strong interest in how the key fishing grounds of the North Sea are managed. There is still the possibility that the government will choose to remain part of the EU common fisheries policy, or abide by its quota limits from the outside, in order to avoid a situation of conflict over the existing stocks.

The Department for Environment, Food and Rural Affairs said: “The UK welcomes the vote on the North Sea Multi-Annual Plan which aims to secure the long-term sustainability of North Sea fish stocks and provide stability for fishermen in the region. As we leave the European Union, we will continue to work closely with our neighbours to champion sustainable fishing. Once we have taken back control of our waters, we will be able to ensure our fish stocks are managed more sustainably while also helping the UK fishing industry to thrive.”

Andrew Clayton, project director at the Pew Trusts, said: “MEPs have again stepped in to defend the ambitious fisheries reforms the EU agreed four years ago, and hold reluctant fisheries ministers to account on their commitments. This multi-annual plan has the potential to end overfishing in the North Sea and provide healthy stocks and productive fisheries. Now fisheries ministers need to make more urgent progress in delivering this.”

At present, more than 40% of fish stocks in the North Sea – the most productive sea in Europe – are overfished. Scientists estimate that if managed sustainably, stocks could produce an additional 1.45m tonnes of fish a year within the next 10 years. Key species could fare well under a stock protection programme, meaning catches of cod and haddock could be increased fourfold within a decade.

However, if the UK opts to leave the CFP as part of Brexit, there could be increased pressure on fish stocks as sustainability targets agreed by the EU would no longer be binding, and EU fisheries ministers would come under pressure from their domestic fishing fleets to allow greater catches in order to compete with the UK.

Environmental campaigners fear that the slow progress towards recovering fisheries stocks, hard won over the last two decades, could be wiped out in such a scenario.