Police discovered a wooden ship carrying the corpses of seven men on a beach in Ishikawa prefecture last week.
Inside the boat they also found a badge with the likenesses of North Korean leaders Kim Jong Il and Kim Il Sung, along with a cigarette box with Korean letters, officials said.
Last year, 104 so-called "ghost ships" were recorded
, officials said, many with the corpses of their former crews on board.
The ship found in Ishikawa was the first in 2018 found carrying dead bodies, though eight other vessels have also washed up.
On the same day, a man's body was also found on the same beach, about 15 meters away from the boat.
It is believed the vessels are coming from North Korea, based on markings and belongings found on the boats, as well as a handful of crew who have survived. Hunger and desperation are thought to be driving them further out to the choppy seas between the Korean Peninsula and Japan.
"Generally speaking the winter ocean in (those seas) is very rough, and the tougher winter brings more shipwrecks," an official from the Japanese Coast Guard told CNN last year.
North Korea is more than 1,000 kilometers (600 miles) from Japan and many of the North Korean boats drifting onto Japanese beaches are ill-equipped to travel such a vast distance across open sea.
Some experts argue that the surge in "ghost ships" is tied to new pressure from the North Korean government, which may be prompting fishermen to go dangerous distances to haul in their catch.
"Fish are a vital resource for North Koreans because they are the cheapest source of protein and they can sell it to China for cash," said Ma Chang-mu, a senior researcher at the Korea Maritime Institute in South Korea.
According to the Korea Institute for International Economic Policy, North Korean seafood exports to China surged 88% in the first half of 2017, compared to the same six months in 2016.
Another factor may be overfishing in North Korean coastal areas. Researchers said Pyongyang granted fishing rights to Chinese companies years ago, leading to depleted fish stocks in nearby waters.
Analysts said North Korean fishing ships often offload their catches on the high seas
, allowing them to be labeled as caught by other nations and get around the stringent international sanctions placed on Pyongyang.
The problem isn't limited to Japan. On January 7, authorities on South Korea's eastern coast discovered an overturned North Korean wooden fishing vessel with the bodies of four men on board.
At inter-Korean negotiations taking place along the demilitarized zone
(DMZ) on Wednesday, delegations agreed to organize the repatriation of the four bodies to North Korea.
The bodies are to be transferred via the Panmumjom border complex Thursday morning.