Kubodera, a squid specialist, also filmed what he says was the first live video footage of a giant squid in 2006, but only from his boat after it was hooked and brought up to the surface.
"Researchers around the world have tried to film giant squid in their natural habitats, but all attempts were in vain before," Kubodera said.
"With this footage we hope to discover more about the life of the species," he said, adding that he planned to publish his findings soon.
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Kubodera said the two successful sightings of the squid -- in 2012 and 2006 -- were both in the same area, some 1,000 kilometres south of Tokyo, suggesting it could be a major habitat for the species.
The giant squid, "Architeuthis" to scientists, is sometimes described as one of the last mysteries of the ocean, being part of a world so hostile to humans that it has been little explored.
Researchers say Architeuthis eats other types of squid and grenadier, a species of fish that lives in the deep ocean. They say it can grow to be longer than 10 meters.