The trio was arrested for stealing a generator from a hut on the island amid a mysterious spike in North Korean boat arrivals in Japan.
The boat was spotted moored off the coast of the deserted island near Hokkaido, Japan.
Several members of the 10-strong crew admitted taking electrical equipment from the hut, with three being arrested.
The remaining seven sailors were sent to the Immigration Bureau.
It is not thought the crew were trying to defect.
The number of arrivals, dubbed “ghost boats” found adrift and or grounded on the Japanese coast has skyrocketed from four in November 2016 to 28 last month.
Experts claim the boats are simply carrying fishermen and soldiers drafted in to help fish amid widespread food shortages in Kim Jong-un’s communist paradise.
The latest arrival comes just days after the bodies of three North Koreans were found off the coast of Japan shortly after an abandoned boat was discovered.
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 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.
Coastguard officials have recovered at least 18 bodies this year.
Last week, a wooden vessel was discovered by the Japan Coast Guard on the western shore of Sado – the island in the Sea of Japan is 450miles from North Korea.
Cigarettes and life jackets appeared to feature Korean lettering, suggesting the ship set sail from the hermit kingdom.
Japanese authorities are also holding 18 people from two other boats, who claim to be North Koreans and reportedly wish to return to the dictatorship.
Experts have pointed to food shortages in the rogue state as a reason boats are having to sail further in an attempt to bring in a higher fishing yield.