The pair were researching violent trauma on skeletal remains of prehistoric hunter-gatherers when they came across the finding.
The research was published in Journal of Archaeological Science: Reports.
"We were initially flummoxed by what could have caused at least 790 deep, serrated injuries to this man," said the researchers. "There were so many injuries and yet he was buried in the community burial ground, the Tsukumo Shell-mound cemetery site."
They continued, "The injuries were mainly confined to the arms, legs, and front of the chest and abdomen. Through a process of elimination, we ruled out human conflict and more commonly-reported animal predators or scavengers."
The pair worked with expert George Burgess, Director Emeritus of the Florida Program for Shark Research, to put together a reconstruction of the attack. They concluded that the individual died between 1370 to 1010 BC, more than 3000 years ago.
The team believes he was alive at the time of the attack, his left hand being torn off as a possible defense wound. The body was also missing the right leg, and the left leg was placed on top of the body.
According to the team, "given the injuries, he was clearly the victim of a shark attack. The man may well have been fishing with companions at the time, since he was recovered quickly. And, based on the character and distribution of the tooth marks, the most likely species responsible was either a tiger or white shark."
Co-author Dr Mark Hudson, a researcher with the Max Planck Institute, said, "the Neolithic people of Jomon Japan exploited a range of marine resources... It’s not clear if [the individual] was deliberately targeting sharks or if the shark was attracted by blood or bait from other fish. Either way, this find not only provides a new perspective on ancient Japan, but is also a rare example of archaeologists being able to reconstruct a dramatic episode in the life of a prehistoric community."