Officials from the Japanese Coast Guard (JCG) are working to confirm the nationality of the bodies after making the grim discovery.
But they said dozens of boats and bodies discovered drifting in Japanese waters so far this year are believed to have set sail from North Korea.
Experts say food shortages in the secretive state could be behind the string of wrecked or lost boats as Kim Jong-un’s regime imposes harsher quotas and desperate fishermen risk sailing their rickety vessels into more dangerous waters.
The latest ship came ashore 44 miles north of a marina where Japanese police last week found eight men who said they were from the North.
Officers said the crew appeared to be fishermen whose boat, which was found nearby, had run into trouble.
And over the weekend, the bodies of two men, which were also partly skeletonised, were found on the western shore Sado island, in the Sea of Japan.
Officials said they had yet to identify the remains, but North Korean cigarettes and life jackets with Korean writing on them found nearby pointed to the pair’s likely origin.
Seo Yu-Auk, research manager of the North Korean Studies Institution in Seoul, said a lack of food in Kim’s rogue state could be to blame for the spate of lost boats.
He said small and old North Korean ships are heading away from the relative safety of Korean coastal waters into deeper seas where they are far more vulnerable to storms and bad weather.
He said: “North Korea pushes so hard for its people to gather more fish so that they can make up their food shortages.”
A series of crippling sanctions coupled with one of the worst droughts in nearly two decades has threatened to cause extreme hardship for millions of people in large parts of the North.
But despite the international pressure, dictator Kim has continued to plough money into his nuclear and ballistic weapons programmes while leaving millions of people without enough to eat.
And Yoshihiko Yamada, professor at Japan’s Tokai University, warned fishermen in the Sea of Japan – regardless of their port of origin – would need to be extra vigilant at this time of year as conditions worsen.
He said: ”During the summer, the Sea of Japan is quite calm. But it starts to get choppy when November comes.
“It gets dangerous when northwesterly winds start to blow.”
Official figures from the JCG show 43 wooden ships believed to have come from the Korean Peninsula have either washed up or been spotted drifting off the Japanese coast so far this year.
In 2016, a total of 66 ships were found.