But what came next excited him most - hundreds of vivid photos of a rare giant squid in its natural habitat deep undersea.
Observing a giant squid in the wild for the first time, Kubodera's team captured photos of a 8m-long, purplish-red sea monster attacking its bait about 900m undersea, then struggling for more than four hours to get free.
The squid pulled so hard on the line that held the shrimp bait that it severed one of its own tentacles.
"It was quite an experience to feel the still-functioning tentacle on my hand," Kubodera, a researcher with Japan's National Science Museum, said in an interview with reporters.
"But the photos were even better."
The giant squid's severed tentacle
The mysterious giant squids, formally called Architeuthis, have for centuries been the stuff of legend, appearing in the myths of ancient Greece, or attacking a submarine in Jules Verne's 20,000 Leagues Under the Sea.
But they had previously been seen only when they were caught in fishing nets or washed ashore dead or dying - never alive in their natural habitat.
But the Japanese team, capping a three-year effort, filmed the creature in September of the past year, finding what one researcher called "the holy grail" of deep sea animals.
The results were not announced until this week, when they were published in Wednesday's issue of the British journal, the Proceedings of the Royal Society B: Biological Sciences.
- World's largest invertebrates, up to 900kg
- Females up to 18m, males rarely exceed 9m
- Have largest eyes in the animal kingdom, up to 25cm in diameter
- Live in ocean depths down to 1000m
- Diet consists mainly of fish and other squids
- Preyed on by sperm whales and reef sharks
- Have eight arms and two tentacles, used to find food and fight off predators
- Remains of 250 giant squids found dead or dying documented over 150 years
- None ever caught alive
Kyoichi Mori, of the Ogasawara Whale Watching Association, was co-author of the study.
Largely because of the sheer difficulty of finding the deep-sea dwelling giant, the team's photos were cheered by researchers around the world.
"That's getting footage of a real sea monster," said Randy Kochevar, a deep sea biologist with the Monterey Bay Aquarium in California.
"Nobody has been able to observe a large giant squid where it lives. There are people who said it would never be done. It's really an incredible accomplishment."
The photos, taken with strobe lights at 30 second intervals, also shed some new light on the mysterious squid's behaviour.
"We think it is a much more active predator than was previously thought," Kubodera said on Wednesday. "It had previously been seen as more lethargic, and not as strong."
In the pictures, the squid's tentacles can be seen stretching out towards the bait, grasping it and pulling away in a ball.
It is then seen struggling to get itself free of the jig attached to the line under the remote-controlled camera. The struggle took place at a depth of between 600-900m.
Kubodera said catching the squid on film was the result of 10 years of sleuthing. He added that he had some help from a population of sperm whales.
"We knew that they fed on the squid, and we knew when and how deep they dived," he said. "So we used them to lead us to the squid."
Kubodera and his team found the squid about 16km off the remote island of Chichijima, which is about 950km southeast of Tokyo. They had been conducting expeditions in the area for about three years before they actually succeeded in making their first contact at 9.15am on 20 September last year.
"We were very lucky," he said. "A lot of research went into it, but still, others have tried and not succeeded."
Tsunemi Kubodera with a similar
giant squid at a Tokyo museum
Giant squids are the world's largest invertebrates, and can grow to a length of 16m. Kubodera said the one he caught on camera was probably an adult female.
He said the giant squid's tentacle would not grow back, but the squid's life was not in danger.
New Zealand's leading authority on the giant squid, marine biologist Steve O'Shea, praised the Japanese team's feat.
"Through sheer ... determination the guy has gone on and done it," said O'Shea, chief marine scientist at the Auckland University of Technology, who is not linked to the Japanese research.
O'Shea has said he hopes to capture juvenile giant squids and grow them in captivity. He captured 17 of them five years ago, but they died.