Minister for Agriculture, Food and the Marine Michael Creed has said a "discard ban" will come into effect on 1 January, following last night's 2019 EU Fisheries negotiations.
Mr Creed attended the Annual Fisheries Council meeting in Brussels where fish quotas were discussed into the early hours of this morning.
He said it was a difficult issue for the Fisheries Council to deal with and he praised the fishing industry who he said found a way to "make this work".
The talks ended with a "balanced outcome", he said.
The discard ban, known as the landing obligation, will see an end to the practice of discarding juvenile fish at sea.
The department said the application of the ban for all Irish stocks in 2019, coupled with a move towards fishing at maximum sustainable yield levels, were "positive developments towards sustainability".
Mr Creed said there were increases in the quota for a number of fish stocks following the talks.
These include increases in Cod, Haddock, Hake, and Megrims in the Celtic Sea. Mr Creed said the increase in quotas was supported by scientific advice for stocks.
However, there was a cut to the prawn quota of 32%, with the minister saying this was in the interest of sustainability and that it reflected scientific advice.
Irish campaigners have said the meeting failed to follow scientific advice on quotas and end EU overfishing of fish stocks such as cod, herring and critically endangered eel.
Rebecca Hubbard of the Our Fish campaign said that this should have been the year EU ministers would end overfishing.
"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," she said.
"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."
Across the sea in Scotland, the deal has been described as "less than what was hoped" for Scottish vessels.
Industry bodies claimed the deal was "challenging but acceptable" and highlighted the need to leave the Common Fisheries Policy.
These were the final fisheries negotiations before the UK is set to leave the EU.
Mike Park, 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 and the fact that this is our last fisheries council as a fully-fledged member state.
"The outcome is less than what we hoped but as much as was possible under the circumstances."
Bertie Armstrong, chief executive of the Scottish Fishermen's Federation, said the talks were difficult with the additional element this year of politics related to Brexit.
For the Scottish industry, the central issue has been the inclusion of measures to limit the risk of 'chokes' by swapping between member states.
He added: "In the end, it is clear that our best interests can only be put first when we have left the CFP and are able to decide who catches what, where and when in UK waters."
December Council is the culmination of all the year-end negotiations where fishing policies are finalised.
Each member state is allocated quotas for each stock. This caps the amount the industry is able to fish for each stock.
The quotas look to balance scientific advice and the need for sustainable fishing, with economic interests.