The deal, which needs the approval of the European Parliament, could end haggling over annual fishing quotas and introduce long-term plans to grow fish stocks.
It will overhaul the Common Fisheries Policy, which dates from the 1970s and is widely regarded as a failure for allowing subsidised, industrial-sized fleets to devastate fish stocks.
The deal, which took 36 hours of negotiations until dawn on Wednesday (15 May), will introduce a ban on the practice of throwing undersized or unwanted fish back into the sea, often to die.
This would apply to mackerel and herring by 2015 and for other species from 2016. Some fish will be exempt.
Simon Coveney, the Irish agriculture and fisheries minister, had worked to find a compromise between the Council and the European Parliament, which had voted for tougher curbs on fishing.
“This agreement follows very difficult and complex negotiations, it amounts to a significant compromise on behalf of my fellow fisheries ministers to allow further negotiations with the European Parliament take place to finalise the reform of the Common Fisheries Policy in the coming weeks,” said the minister, who headed the negotiations under Ireland’s rotating presidency of the EU Council.
“This decision by the Council is a major conciliatory step in the direction of the European Parliament and hopefully paves the way for successful conclusion of the inter-institutional negotiations on the reform,” he said.
About 80% of Mediterranean and 47% of Atlantic stocks are overfished, European Commission figures showed.
Campaign groups expressed disappointment and said they believed it would take longer than expected to replenish stocks. A World Wide Fund for Nature report said it would take more than 100 years for fish stocks to recover.
Saskia Richartz, Greenpeace EU fisheries policy director, was among those expressing disappointment with the deal and urged the Parliament to reverse course.
"The Parliament will need to decide whether to continue negotiations on the basis of this take-it-or-leave-it proposal from the Council. It must continue to represent the political and public support behind the recovery of our oceans for Europe to be able to safeguard its marine environment and keep its sustainable fishing sector alive,” Richartz said.