Minster for Agriculture Michael Creed has said that the decision by the British government to withdraw the UK from the London Fisheries Conventions is "unwelcome and unhelpful".
The move will mean that trawlers from the Republic of Ireland will no longer be allowed to fish within 12 nautical miles of the UK coastline.
British ministers will trigger withdrawal from the London Fisheries Convention, signed in 1964 before the UK joined the European Union, to start the two-year process to leave the agreement.
In a statement, Mr Creed said the announcement is a "part of Brexit" and it will be considered by the EU 27 nations and chief Brexit negotiator Michel Barnier when the negotiations commence.
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"The announcement will have no immediate effect as the withdrawal process from the Convention will take two years and will form part of the Brexit negotiations," said Mr Creed.
The convention allows vessels from the Republic of Ireland, France, Belgium, Germany and the Netherlands to fish within six and 12 nautical miles of the UK's coastline.
It sits alongside the EU Common Fisheries Policy which allows all European countries access between 12 and 200 nautical miles of the UK and sets quotas for how much fish nations can catch.
Mr Creed said Brexit poses a "very serious challenges to the seafood sector and this announcement will form part of the negotiations".
British ministers claimed the move would help take back control of fishing access to UK waters, as it will no longer be bound by existing access agreements, and enable the country to become fully responsible for fisheries management.
UK vessels will also lose the right to fish in the waters six to 12 nautical miles offshore of the other countries.
British Environment Secretary Michael Gove said: "Leaving the London Fisheries Convention is an important moment as we take back control of our fishing policy. It means for the first time in more than 50 years we will be able to decide who can access our waters.
"This is an historic first step towards building a new domestic fishing policy as we leave the European Union - one which leads to a more competitive, profitable and sustainable industry for the whole of the UK."
The UK fishing industry was made up of more than 6,000 vessels in 2015, landing 708,000 tonnes of fish worth £775m.
Some 10,000 tonnes of fish was caught by other countries under the convention, worth an estimated £17m.