Other scientists involved in the expedition this summer, which logged 400 hours of dives, were American oceanographer and marine biologists Edith Widder and Steve O'Shea from New Zealand.
NHK said a high-definition camera was developed for the project that could operate deep in the ocean and used a special wavelength of light invisible to the giant squid's sensitive eyes.
Kubodera said scientific research, technology and the right lure all came together to make the encounter possible, and that this case will shed more light on deep-sea creatures going forward.
After more than a decade of going out to sea in search of the giant squid, he relished the moment he came face-to-face with it.
"It appeared only once, out of 100 dives. So perhaps, after over 10 years of some kind of relationship I've built with the giant squids, I feel, perhaps, it was the squid that came to see me."
Associated Press writer Emily Wang contributed to this report.