Bluefin tuna stocks in the Atlantic and Mediterranean have crashed in recent years, with populations declining by up to 80 per cent from only three or four decades ago.
Japan, which buys three-quarters of the global catch of bluefin tuna, had lobbied extensively in Doha and elsewhere to block the proposal.
Tokyo expressed willingness to accept lower quotas but wanted those to come from the International Commission for the Conservation of Atlantic Tunas (Iccat), which currently regulates the trade.
Masanori Miyahara, chief counsellor of the Fisheries Agency of Japan, said that Japan is "very serious" about measures to conserve the Atlantic bluefin tuna and aims to "ensure the recovery of the stock".
Commenting on the vote, Sue Lieberman, policy director for the Pew Environment Group in Washington, said: "This is very disappointing and very irresponsible."
Lieberman said "the fate of tuna is now, once again, in the hands of Iccat" which has "demonstrated over a period of decades" its inability to enforce its own quotas for tuna catches.