The deal, agreed in London on Wednesday -- a week after negotiations with Iceland broke down -- is aimed at ending a four-year "mackerel war" over north Atlantic mackerel quotas with Iceland and the Faroe Islands, an autonomous Danish territory.
"I would have preferred that Iceland joined the agreement but an agreement between three is a big step in the right direction," Norwegian Minister of Fisheries Elisabeth Aspaker said in a statement.
Iceland's Foreign Minister Gunnar Bragi Sveinsson expressed surprise that the deal had gone ahead without his country's involvement.
"What we have been wondering is what secret deals were going on while we believed we were in an honest and open discussion with the European Union and the Faroe Islands," he said. "It seems that behind the scenes another deal was being negotiated behind our backs and it has reached the surface now."
Previous negotiations collapsed on March 5 with Iceland and Norway -- both non-EU states -- blaming each other for the failure.
The five-year agreement allows the EU a 611,000 tonne mackerel quota, while Norway gets 279,000 tonnes and the Faroes 156,000 tonnes.
"This agreement ensures the long term sustainability of this valuable stock," EU Commissioner for Maritime Affairs and Fisheries, Maria Damanaki said in a statement, adding that a "reserve" quota had been set aside for Iceland.
"The door is still open for Iceland to join the other parties in the near future."
The issue of quotas heated up in recent years as mackerel started migrating north to the fishing waters off the Faroes and Iceland in response to rising sea temperatures.
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When Iceland and the Faroe Islands unilaterally increased their quotas in 2010 Brussels responded with sanctions against the Faroe Islands for overfishing herring, banning imports of both mackerel and herring from the archipelago and forbidding some of its fishing boats from docking in EU ports.
Iceland has not suffered any sanctions so far but fishing has been a major obstacle stopping the island nation from joining the EU.
Reykjavik pulled out of accession talks indefinitely in September despite public support for a promised referendum on joining the bloc.