The vessel -- a 12.5-meter long wooden boat -- was found on Sunday 10km (6.2 miles) south of the Ushitaki fishing port in Sai Village, Aomori prefecture, a spokesman for the Aomori Coast Guard told CNN Monday.
Though there was nothing to definitively identify the boat, it looks very similar to boats found in October in the same region, which featured Korean "Hangul" lettering and markings on their hull, he said, adding that they may have come from North Korea.
The condition of the latest boat indicated it may have been drifting for some time, he said.
Over the past two months, at least 12 wooden boats have been found adrift along Japan's coast carrying chilling cargo -- the decaying bodies of 22 people, according to police and Japan's coast guard.
All the bodies were "partially skeletonized" -- two were found without heads -- and one boat contained six skulls, the coast guard said. The first boat was found in October, then a series of boats were found in November.
Coast guard officials are trying to unravel the riddle of where these ghostly boats came from and what happened to those on board. Their best guess so far is that the ships are from North Korea.
One clue pointing that direction is the same Korean lettering on the hull of a boat containing 10 decomposing bodies, one of three boats that were found adrift off the city of Wajima on the west coast of Japan on November 20.
The writing said "Korean People's Army," the name of North Korea's military defense forces, the coast guard said.
Another clue could come from a tattered scrap of cloth found on one of the boats, which looks like it could be from a North Korean national flag, Japan's biggest broadcaster NHK reported.
But what the boats are is a mystery.
Some in the Japanese media believe the vessels were fishing vessels that strayed off course, while others suggest they could be transporting defectors.
"What we do know is that for those people living outside of (North Korean capital) Pyongyang ... life remains extraordinarily hard, and it may be an economic necessity as much as a desire for political freedom (that is) encouraging some people in the North to try and leave the country," John Nilsson-Wright, head of the Asia program at the Chatham House policy institute, told CNN last week.
He added that defectors could be taking the more dangerous route across the Sea of Japan -- also known as the East Sea -- because traditional routes, like crossing the border into China, are now policed and could be harder to use.
But he conceded that it was impossible to know for sure given the limited information available.