A Japanese fishing boat recovered a male body floating off the coast of Sakata, Yamagata, and two more bodies washed up on a nearby beach an hour and a half later, the coastguard said.
They added although the bodies were decayed, but one had a lapel pin thought to be North Korean.
Officials are investigating if the bodies were from the severely damaged boat that washed ashore on Saturday.
Winds and water currents push dozens of boats onto Japan’s northern coasts annually.
Rickety North Korean fishing boats are particularly vulnerable because they lack the sturdiness and equipment to return home.
But the alarming number over the last few weeks has prompted Japanese authorities to step up patrols.
28 of the vessels, dubbed “ghost boats”, were detected in November, up from just four in November last year.