On a gloomy day pregnant with rain and the weight of past expectations, tuna fisherman Minoru Nakamura is welcomed back to port by his family in Ishiki like a conquering hero.

Three generations wait onshore, including Mr Nakamura's father Toshiaki and newborn child Misaki, smiles wide and cameras primed, as his boat sails into harbour. On this remote island off southern Japan, where rusting boats wait for fishermen who increasingly stay at home, few sights excite more than Mr Nakamura's precious cargo: a 172kg (380lb) bluefin tuna, splayed across the deck of his small trawler.

Mr Nakamura has been dubbed Japan's King of Fish. At peak prices his single catch will fetch over 1.5m yen, (£10,600) at the world's biggest fish market in Tsukiji, Tokyo. By the time it is carved up and sold as thousands of sushi, sashimi and steak cuts to restaurants across the capital, it will be worth at least three times that much – the price of a luxury family car.

But among many of Ishiki's 32,000 population, one-in-eight of whom depend on the sea to survive, the talk is of now one thing: the extinction of their livelihood. "In 40 years on a boat I've never seen it so bad," says one inhabitant, Yoshiju Kukeya. "Nakamura-san is lucky today. The fish are not there any more."

Atsushi Sasaki, 61, a fisherman-turned-conservationist who is sounding the alarm bell increasingly desperately about Japan's and the world's free-falling tuna stocks, speaks of imminent extinction: "If the situation continues, it is inevitable that tuna will disappear from the seas."

A string of doomsday predictions about the fate of the Pacific tuna led Japan's largest fisheries cooperative this summer to announce an unprecedented suspension of operations. This week, an international preservation group meeting in Morocco warned that once-teeming stocks of bluefin tuna in the Atlantic Ocean and Mediterranean have plummeted by 90 per cent and may shortly be put on the official endangered list.

Most of the blame has been heaped on Japan, which consumes about three-quarters of the world's bluefin, according to Greenpeace, and increasingly imports what it cannot catch (currently about 44,000 tonnes a year). But the global spread of healthy Mediterranean and Japanese cuisine, and exploding consumption in China and Russia, is also helping to drive the species towards extinction.

Until 30 years ago, tuna was considered so worthless by many trawlers that it was thrown back into the sea or processed for cat-food. Nowadays, rocketing prices mean it has attracted the attention of Italian and Russian mafia, who control much of the Mediterranean trade, according to Daniel Pauly, one of the world's top fisheries experts. "Most Japanese people have no idea where their tuna is coming from," he says. "If they did, they might eat a lot less."

Around the coast of Japan in fishing communities like Ishiki, boats are returning to port empty. Terutaka Okubo, head of the local fishing co-operative, shows on spreadsheet in his office the stunning decline in tuna catches: down to a quarter of their 2005 levels. He says that Mr Nakamura's haul is the first tuna weighing in at more than 150kg to be caught this year. Last year there were more than 100. "It began a few years back but it is now really striking," he explains. "Smaller fish are coming in because they're all that are left."

Mr Sasaki explains the implications: "Tuna under 36kg are incapable of producing babies, so the fishermen are cutting their own throats by catching immature fish."

Tough and sinewy, with the leathery skin of a veteran seadog, Mr Sasaki has circled Japan in his trawler on a one-man research mission that has left him deeply pessimistic that voluntary suspensions of fishing will succeed. "The government must bring in much tougher regulations. At the moment, it's a free-for-all," he says.

Later, he sails his boat into the choppy seas an hour off Ishiki, to a narrow channel, crowded with boats like his, sinking single lines into the sea. He bitterly condemns net fishing, which he calls "the enemy", because the nets haul in the baby fish and smaller tuna, and are virtually unregulated.

"We can't do much damage with single lines," he says as he rigs up the first of several rods. "This is the only way that tuna fishing can be sustainable. We catch one at a time." Like all the fishermen here, he speaks of the "romanticism" of the tuna. "It's big and powerful and it stirs boys' imaginations. There's no other fish like it."

Seven hours later, he returns to port empty-handed, his worst fears again confirmed. "If the fish are no longer there, Japan will starve," he says.

The disappearing tuna, and rising fuel prices, are keeping fishermen at home and putting youngsters off the industry. Meanwhile, some of Ishiki's men opt to work 12 or more hours a day to make up for the declining catch.

Others have shifted to other fish like saury or sardines in an effort to make a living. The ripples from the crisis around Japan's coastline are already being felt on the nation's restaurant tables. Some sushi chefs have switched to using alternative fish and ingredients.

Few Japanese want to contemplate the disappearance of the beloved dinner-table favourite, but unless the country takes drastic action, they may have no choice, warns Mr Sasaki. Farming tuna makes the problem worse because it entails robbing the seas of young fish, he argues."We have to learn to hunt sustainably and eat less. There is just no other solution."

Some Ishiki fisherman estimate their income has halved in a year due to the overfishing of overstretched stocks. "Nobody wants to really face up to what might happen," says Hiroyuki Yoshihara, 38, who has a young family. "We joke about it, but if something doesn't change we won't be here in 10 years, but we don't know how to do anything else."