KUSHIMOTO, Japan— Tokihiko Okada was on his boat one recent morning when his cellphone rang with an urgent order from a Tokyo department store. Its gourmet food section was running low on sashimi. Could he rustle up an extra tuna right away?

Mr. Okada, a researcher at Osaka’s Kinki University, was only too happy to oblige—and he didn’t need a fishing pole or a net. Instead, he relayed the message to a diver who plunged into a round pen with an electric harpoon and stunned an 88-pound Pacific bluefin tuna, raised from birth in captivity. It was pulled out and slaughtered immediately on the boat. Not long ago, full farming of tuna was considered impossible. Now the business is beginning to take off, as part of a broader revolution in aquaculture that is radically changing the world’s food supply. “We get so many orders these days that we have been catching them before we can give them enough time to grow,” said Mr. Okada, a tanned 57-year-old who is both academic and entrepreneur. “One more year in the water, and this fish would have been much fatter,” as much as 130 pounds, he added. With a decadeslong global consumption boom depleting natural fish populations of all kinds, demand is increasingly being met by farm-grown seafood. In 2012, farmed fish accounted for a record 42.2% of global output, compared with 13.4% in 1990 and 25.7% in 2000. A full 56% of global shrimp consumption now comes from farms, mostly in Southeast Asia and China. Oysters are started in hatcheries and then seeded in ocean beds. Atlantic salmon farming, which only started in earnest in the mid-1980s, now accounts for 99% of world-wide production—so much so that it has drawn criticism for polluting local water systems and spreading diseases to wild fish. Until recently, the Pacific bluefin tuna defied this sort of domestication. The bluefin can weigh as much as 900 pounds and barrels through the seas at up to 30 miles an hour. Over a month, it may roam thousands of miles of the Pacific. The massive creature is also moody, easily disturbed by light, noise or subtle changes in the water temperature. It hurtles through the water in a straight line, making it prone to fatal collisions in captivity.

Your browser does not support the audio element. Scroll A view of the bay in Kushimoto, Japan, where bluefin tuna are raised. Jeremie Souteyrat for The Wall Street Journal A view of the bay in Kushimoto, Japan, where bluefin tuna are raised. Scroll Tokihiko Okada, general manager of the Oshima Station of the Kinki University Fish Nursery Center, heads out to catch farm-raised bluefin tuna, after receiving an order from a high-end department store in Tokyo. Jeremie Souteyrat for The Wall Street Journal Tokihiko Okada, general manager of the Oshima Station of the Kinki University Fish Nursery Center, heads out to catch farm-raised bluefin tuna, after receiving an order from a high-end department store in Tokyo. Scroll Pens at the Kinki University Fish Nursery Center are used to raise bluefin tuna. Luis Patron for The Wall Street Journal Pens at the Kinki University Fish Nursery Center are used to raise bluefin tuna.

The Japanese treasure the fish’s rich red meat so much that they call it “hon-maguro” or “true tuna.” Others call it the Porsche of the sea. At an auction in Tokyo, a single bluefin once sold for $1.5 million, or $3,000 a pound. All this has put the wild Pacific bluefin tuna in a perilous state. Stocks today are less than one-fifth of their peak in the early 1960s, around the time Japanese industrial freezer ships began prowling the oceans, according to an estimate by an international governmental committee monitoring tuna fishing in the Pacific. The wild population is now estimated by that committee at 44,848 tons, or roughly nine million fish, down nearly 50% in the past decade. The decline has been exacerbated by earlier efforts to cultivate tuna. Fishermen often catch juvenile fish in the wild that are then raised to adulthood in pens. The practice cuts short the breeding cycle by removing much of the next generation from the seas. Net pens, originally developed by Teruo Hara, are seen in this photo taken in the 1950s. The pens improved the efficiency of fish farming dramatically compared with the preceding era, when fish were kept in much larger spaces in the bay created by simple partitions. Kinki University Scientists at Kinki University decided to take a different approach. Kinki began studying aquaculture after World War II in an effort to ease food shortages. Under the motto “Till the Ocean,” researchers built expertise in breeding fish popular in the Japanese diet such as flounder and amberjack. Hidemi Kumai, an emeritus professor at Kinki University and former head of the bluefin tuna farming department. Jeremie Souteyrat for The Wall Street Journal In 1969, long before the world started craving fresh slices of fatty tuna, Kinki embarked on a quest to tame the bluefin. It sought to complete the reproduction cycle, with Pacific bluefin tuna eggs, babies, juveniles and adults all in the farming system. Two scientists from Kinki went out to sea with local fishermen, seeking to capture juvenile tuna for raising in captivity. “We researchers always wanted to raise bluefin because it’s big and fast. It’s so special,” said one of the scientists, Hidemi Kumai , now 79 years old. “We knew from the beginning it was going to be a huge challenge.”

Watch a video about Kinki University’s tuna farming operation in Kushimoto, Japan.

It was more than that. The moment the researchers grabbed a few juvenile fish out of a net, the skin started to disintegrate, killing them. It took four years just to perfect delicate fast-releasing hooks for capturing juveniles and moving them into pens. “Local fishermen used to say to us, ‘Professors, you are crazy. Bluefin can’t live in confinement,’ ” Mr. Kumai recalled. In 2011, Kinki lost more than 300 grown fish out of is stock of 2,600 after an earthquake-triggered tsunami hit a coastline 400 miles away. The tsunami triggered a quick shift in tide and clouded the water, causing the fish to panic and smash into nets. Last year, a typhoon decimated its stock. Again this summer, frequent typhoons kept the researchers on their toes as they waited for the breeding season to start. “Oftentimes, all we can do is pray,” said Mr. Okada as he threw a mound of mackerel into the pen using a spade. It took nearly 10 years for fish caught in the wild to lay eggs at Kinki’s research pens. Then, in 1983, they stopped laying, and for 11 years, researchers couldn’t figure out the problem. The Kinki scientists now attribute the hiatus to intraday drops in water temperature, a lesson learned only after successful breeding at a separate facility in southern Japan. In the summer of 1994, the fish finally produced eggs again. The researchers celebrated and put nearly 2,000 baby fish in an offshore pen. The next morning, most of them were dead with their neck bones broken. The cause was a mystery until a clue came weeks later. Some of the babies in the lab panicked when the lights came on after a temporary blackout and killed themselves.

Samples of tuna in early stages of their life cycle are preserved in bottles at the Kinki University Fish Nursery Center. Jeremie Souteyrat for The Wall Street Journal

Mr. Kumai and colleagues realized that sudden bright light from a car, fireworks or lightning caused the fish to panic and bump into each other or into the walls. The solution was to keep the lights on at all times. “ These fish can’t protest with their mouths so they protest by dying. ” — Hidemi Kumai For nearly five decades, Mr. Kumai has lived along a quiet inlet, steps from the university’s research pens. He calls the fish “my family.” “These fish can’t protest with their mouths so they protest by dying,” he says. “We must listen to them carefully so we catch the problems before they resort to dying.” At last, in 2002, the Kinki team became the first in the world to breed captive bluefin from parents that were themselves born in captivity. The circle was complete. But the survival rate remained low. While farmed Atlantic salmon had developed into a multibillion-dollar business, it seemed doubtful for years that the tuna undertaking could be commercially viable. Kinki University had funded its project with proceeds from the sale of more common fish raised at its research facilities. That kept the tuna farming alive even after other academic and commercial organizations gave up. Now the university needed help from someone with deeper pockets, and by the latter half of the last decade the timing was right. The world’s voracious appetite for sushi and gourmet fish was eroding stocks of bluefin tuna and governments were beginning to clamp down on overfishing. The country most at risk of a tuna shortage was Japan, which consumes 80% of the world’s overall catch, or some 40,000 tons annually. Japanese trading companies with big fisheries operations such as Mitsubishi Corp. and Sojitz Corp. began courting the Kinki researchers. One early supporter was a young employee of Toyota Tsusho Corp., a trading company affiliated with the auto maker. Taizou Fukuta was working at a desk job in the company’s finance department in Nagoya when he saw a documentary about the tuna project. He was inspired to propose a tuna farming business in a Toyota in-house venture contest and won, according to Mr. Fukuta. With $1 million in seed money, Mr. Fukuta, now 39, visited Kinki’s Mr. Okada, the university’s head of tuna research, many times until the academic agreed to team up with Toyota in 2009. “I was truly impressed by their insistence on sticking with this project for over 30 years,” says Mr. Fukuta, who is now team leader of the company’s agriculture and aquaculture business. Toyota footed the bill for larger facilities where baby fish hatched at the university’s labs could be raised in large numbers for about four months. At that point, the juvenile fish are stable enough to be sold to commercial tuna ranches, where they are fattened in round pens around 100 feet in diameter and 30 feet deep for three to four years before being sold for slaughter. Mr. Fukuta gave up his desk job and moved to a small island off the southern island of Kyushu that offered a warm climate ideal for raising baby tuna. He persuaded local fishermen to lease his company the rights to set up dozens of fish pens. He learned to dive and to steer a boat.

Your browser does not support the audio element. Scroll Mr. Okada, the general manager of Oshima Station, tosses fish into a pen to feed the tuna. Luis Patron for The Wall Street Journal Mr. Okada, the general manager of Oshima Station, tosses fish into a pen to feed the tuna. Scroll A 7-year-old bluefin tuna swims in a pen at the Kinki University Fish Nursery Center. These tuna will spawn eggs for the next generation of farmed tuna. Jeremie Souteyrat for The Wall Street Journal A 7-year-old bluefin tuna swims in a pen at the Kinki University Fish Nursery Center. These tuna will spawn eggs for the next generation of farmed tuna. Scroll After a bluefin tuna is slaughtered, it is immediately dumped in ice. Jeremie Souteyrat for The Wall Street Journal After a bluefin tuna is slaughtered, it is immediately dumped in ice. Scroll Bluefin tuna are packed in ice before shipping to preserve the freshness and pink-red color of the meat. Jeremie Souteyrat for The Wall Street Journal Bluefin tuna are packed in ice before shipping to preserve the freshness and pink-red color of the meat.