British fishermen will face annual negotiations to secure their fishing rights in shared waters from 2020, while other EU countries may lose many of their current rights to fish in British waters, according to a government white paper on fishing after Brexit.

Sustainable Fisheries for Future Generations, published on Wednesday, provided the first glimpse into how the UK’s fishing industry will change after Brexit. Its premise, to be introduced in a fisheries bill, is that the UK should have full control of its waters and the ability to set its own quotas for UK-based vessels.

The government also promised to end the wasteful practice of discarding fish, which has been a by-product of the current quota system.

EU-based fleets land about eight times as much fish in UK waters as British fishermen do in EU waters, under the common fisheries policy, and the government has indicated that this access will be one of the key items under review.

The paper promises a “fairer share” for UK fleets, instead of the “poor deal” they currently have.

Annual statements on the state of fishing stocks will also be issued, and ministers pledged to ensure stocks were not fished beyond levels from which they could recover to health.

Theresa May promised a “bright future in store … by putting the importance of a healthy marine environment at [the] heart” of policy.

Michael Gove, the environment secretary, added: “We will be able to put in place our own systems, becoming a world leader in managing our resources while protecting the marine environment.

The discarding of fish, a by-product of the EU quotas system, was used in pro-Brexit campaigns. AFP/Getty image. Photograph: Daniel Leal-Olivas/AFP/Getty Images

“We will work closely with everyone who has an interest in this important industry to make the most of this historic opportunity.”

The UK’s fishing industry employs about 11,000 people, but, despite its small economic size, became totemic in the referendum campaign, with leave groups arguing the UK’s fleet was unfairly disadvantaged.

The government has control over where it allocates the UK’s quota under the EU rules, and has tended to favour bigger foreign-owned vessels over smaller UK boats.

As part of changes to the EU’s common fisheries policy, the old system of gruelling annual negotiations in Brussels over quotas is being phased out in favour of “multiyear plans” based on scientific advice as to the maximum sustainable yield.

This is intended to give fishing fleets the ability to plan and invest in vessels, equipment and labour, and to protect vulnerable stocks. But according to the white paper, the UK will instead follow Norway’s example in re-examining fishing rights every year.

This is complex, however, as many of the UK fleet’s key fishing grounds such as the North Sea, the Channel and the Irish Sea are shared. Britain will face tough annual renegotiations, as EU member states do not want to give up their lucrative rights in shared fishing grounds.

One of the methods for deciding UK fishing rights set out in the white paper is for “zonal attachment”, by which scientists examine where fish are congregated, instead of basing their calculations on landing data.

Another proposal would tackle the problem of “choke species”, which arises when vessels are fishing mixed grounds containing several species but must stop fishing when they have reached their quota for the most vulnerable stocks, for fear of breaching the law. This can prevent fishermen from fulfilling their quota for less vulnerable species.

Fishing industry groups welcomed the plans. Barrie Deas, the chief executive of the National Federation of Fishermen’s Organisations, called the white paper “clear and cogent, and aligned with international law”.

He said it would enable “effective and adaptive management measures for our fisheries”.

Bertie Armstrong, the chief executive of the Scottish Fishermen’s Federation, said: “[This will allow] the UK to become an independent coastal state, to take charge of who catches what where and to resist any and all attempts to link access to our waters to access to EU markets [for the export of British fish].”

Conservationists warned that the government’s promises on sticking to strict fishing limits to ensure healthy stocks must be enshrined in law.

Dr Lyndsey Dodds, the head of marine policy at WWF, said: “We don’t want to see a ‘fill your boots’ fisheries policy that decimates our precious seas and cripples our fishing communities. Proposals must put the right focus on managing fish stocks in a sustainable way and protecting our marine environment.

“As we leave the EU we must use our power wisely and ensure any increase in fishing doesn’t threaten our marine environment. That means there must be clear commitments to a healthy ocean, underpinned in law in the forthcoming fisheries bill.”

The white paper will be subject to a 10-week consultation.