The boat washed ashore on Japan's Sado Island, northwest from the mainland, on Friday and authorities gained access on Saturday.
The heavily damaged vessel had Korean lettering painted on its side.
Police could not confirm whether the two heads belonged to the corpses but Japanese media said the remains were "partially skeletonised".
This could indicate the victims had been at sea for a long time.
"Ghost boats" believed to hail from North Korea are a fairly common discovery on Japanese shores.
They are generally empty or contain only human remains. During winter, exposure and starvation are the most likely explanations for crewmembers' deaths.
In previous incidents there has been speculation that crew found on the "ghost boats" are defectors or spies from North Korean leader Kim Jong-un's repressive regime.
But it is also thought that poverty is forcing North Koreans to fish further from home.