The EU's executive commission urged EU governments to agree to a temporary ban until the stocks recovered but Greece, Cyprus, Malta, Spain, France and Italy - with strong fishermen's lobbies at home - insisted on continuing the hunt despite the precarious state of the species.
For environmentalists, the move means a further step toward the bluefin tuna's commercial extinction.
"They are pushing tuna to the point of no return," said Xavier Pastor of the Oceana protection group. "It is deplorable that the EU member states who are mostly responsible for the depletion of bluefin tuna stocks refused to agree to a measure that would have helped to reverse the situation."
The EU Commission had hoped the 27-nation bloc could take a united stand at the next meeting of the ICCAT group of nations managing the global stock. Pushing through a ban on fishing bluefin tuna at the group's Nov. 6-15 meeting in Recife, Brazil, now looks unlikely.
"ICCAT members have to realize that the very future of this iconic stock depends on it," said EU Fisheries Commissioner Joe Borg.
Stocks of the threatened bluefin, which have been hunted since Roman times in the Mediterranean, have dwindled for years, with Japan taking some 80 percent of bluefin exports to satisfy demands for the finest raw fish ingredient.
The tuna's uncertain status has driven up prices and prompted fishermen to sidestep stringent quotas to fish illegally for big profits.
Tuna weighing up to 1,100 pounds (500 kilograms) were once found in the Mediterranean, but large fish are now a rarity. Nowadays, fishermen often catch very small tuna before they can reproduce, placing them in cages to be fattened until they are big enough for sale.
The quota for catches was lowered from 28,500 tons to 22,000 this year but scientists still say that is 7,000 tons over what they would advise. A decade ago, 50,000 tons of the fatty, deep-red tuna was hauled in.
Groups like Oceana say illegal fishing has doubled the amount of tuna caught. When the 2007 quota was set at 29,500 tons, Oceana estimates that real catches stood at some 60,000 tons.
Oceana estimates some 45,000 tons of bluefin could be fished sustainably each year if tuna stocks were allowed to recover.
Conservation groups had earlier criticized the EU for not pushing to list the bluefin tuna under the Convention on International Trade in Endangered Species.
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