The discovery comes just days after a group of eight fishermen, who claim to be from North Korea, washed up on Japan's northern coast.
"There were two bodies separately found on the edge of the surf over the weekend," on Sado island in Niigata prefecture, senior local police official Hideaki Sakyo told AFP.
One of the bodies was found early Saturday, with the second corpse discovered yesterday by passers-by who were walking along the beach, which is some 750 kilometres (465 miles) east of North Korea, he said.
However, close to one of the bodies police found 11 boxes of North Korean tobacco as well as boat parts and life jackets with some Korean words written on them, he added.
Separately, authorities discovered a wrecked wooden boat with squid-fishing equipment which again contained some Korean words on Thursday, he said.
"We are investigating the link between the bodies and the boat," Sakyo said.
Dozens of North Korean fishing vessels wash up on Japan's coast every year.
Sometimes the boats' occupants have already died at sea, which local media refer to as "ghost ships."
But their old and poorly equipped vessels are prone to mechanical and other problems, including running out of fuel, and there are few ways for them to call for rescue.
Often surviving drifters are fishermen who request to be sent home, but some of them are defectors who are eventually sent to South Korea.
Japan and North Korea have a tense relationship, with Pyongyang routinely issuing verbal threats as well as firing missiles near or above Japan.
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