Japan’s Coast Guard found the man, who has not been identified, with a pack of cigarettes written in Korean and other personal belongings with Korean written on them the near the body.
The cause of the death is still unknown, the official said.
The discovery was made on Sado Island, more than 40 miles off the North Eastern city of Niigata at around 6:30am on Saturday (21:30 GMT on Friday).
Finding the body will add to the increasing unease in Japan and South Korea over the North’s nuclear arms programme, following Donald Trump’s decision to re-designate the brutal regime as a state sponsor of terrorism.
The discovery marks the third time this month that parts of a wooden boat suspected to be from North Korea have washed up on the shores of Japan.
On Friday, eight “suspicious” North Korean fishermen washed ashore on the coast of northern Japan on Friday.
And earlier this month, the coast guard rescued three North Korean men capsized fishing boat off Japan’s northern coast.
Meanwhile, the reclusive state suffered embarrassment after a defector was filmed escaping the demilitarised zone (DMZ).
Dictator Kim Jong-un was reportedly furious with all of his border guards at the DMZ after being humiliated after a defector escaped into South Korea.
The border guard, known only by his surname Oh, fled by army vehile and then on foot as he was shot at by North Korean guards.