Ministers agreed to limit the cuts to catches proposed by the European Commission in several Northeast Atlantic fisheries such as haddock, herring and plaice, but conservation groups accused them of ignoring data on fish stock sustainability.
French Fisheries Minister Frédéric Cuvillier welcomed the "balanced deal" reached on Thursday (20 December) after two days of quota haggling in Brussels.
"This agreement provides the basis for truly sustainable fishing in the European Union, backed up by indisputable scientific advice," he said in a statement.
A proposed 55% cut in haddock quotas in the Irish Sea, Channel and Bay of Biscay was cut back to 15%, while North Sea plaice catches would fall by 25% next year rather than the 35% proposed by the Commission.
EU Fisheries Commissioner Maria Damanaki said the final deal was not as ambitious as the Commission's original proposal, but described the outcome as satisfactory.
She welcomed a huge improvement in scientific data on stock levels, which meant the EU had clear advice on catch levels for 85% of fish species in 2013, compared with just 39% for this year.
The European Parliament has repeatedly backed the idea of fixing quotas on the basis of long-term management plans for the most important stocks.
However, conservation groups accused ministers of ignoring scientific advice for about half of all fish species covered by the quotas, resulting in catch limits being set above levels that guarantee long-term viability.
"Fisheries ministers are not taking scientific advice into account in their decision-making," conservation group WWF said in a statement.
"As a result every year, just before Christmas, it's a 'fisheries frenzy' where ministers spend days arguing about how much fish can be caught."