* EU wants to protect herring stocks in Northeast Atlantic
* Faroe Islands agrees to new catch-limit for herring
By Anna Nicolaou
BRUSSELS, June 11 (Reuters) - The European Commission could lift its import ban on herring from the Faroe Islands within months after reaching a deal to protect fish stocks in the Atlantic, it said on Wednesday.
EU authorities banned imports of herring and mackerel from the Faroe Islands in August in a row over alleged over-fishing, with the world's biggest fish importer saying it had to protect a fish stock referred to as the Atlanto-Scandian herring.
The Faroe Islands, a self-governed territory within the Danish Realm and not part of the European Union, said at the time that the EU rules do not give it a sufficient share of the herring catch and that a higher quota is justified by an increase in the number of herring in its waters.
On Wednesday, the European Commission said the Faroe Islands had agreed to a new catch limit for Atlanto-Scandian herring. Once that limit is fixed, the EU would end the ban on Faroese herring imports.
"After long and intensive negotiations, I am satisfied that we can soon consider the herring dispute as something of the past," European Commissioner for Maritime Affairs and Fisheries Maria Damanaki said in a statement.
For decades Europe has been taking fish from the sea faster than they can be reproduce themselves, but a reform programme seeks to recover fish stocks and fish at sustainable levels by 2020.
Until 2012, the Atlanto-Scandian herring stock was managed jointly by Norway, Russia, Iceland, the Faroe Islands, and the European Union. Last year, the Faroese unilaterally decided to treble its herring quota, prompting the EU ban of herring and mackerel and preventing some boats from docking at EU ports.
The Faroe Islands, a small archipelago in the north Atlantic Ocean halfway between Norway and Iceland, responded by launching a case with the World Trade Organization (WTO), accusing the EU of violating international maritime law.
The row eased in March, when the EU settled a dispute over mackerel with the Faroe Islands and Norway.
Once the European Union ends its trade ban, the Faroese have agreed to withdraw their case with the WTO, the Commission said.
The Commission says that it has helped cut the number of overfished stocks in the northeast Atlantic to 39 percent from 94 percent in 2005, with all catch limits now decided on the basis of scientific advice.
From 2019, caught fish can no longer be thrown overboard, a rule aimed at encouraging fishermen to be more selective about what they catch and reduce unwanted catches. Caught fish must be used for food or in pharmaceuticals. At the moment, a fifth of caught fish is thrown back into the water. (Editing by Robin Emmott and James Macharia)