It remains unconfirmed whether the bodies are those of the personnel aboard the UH-60JA helicopter, the report said.
Work is underway to bring the bodies to the surface.
The helicopter took off from the Miyakojima base on Miyako Island at 15:46 (06:46 GMT) last Thursday and was due to return to the same base at 17:05, but disappeared from radar shortly after takeoff between Miyako and Irabu islands.
A 24-hour search involving special submersibles, aircraft and patrol boats recovered two life rafts, a door, part of the main propeller, a rotor blade and a fragment of the side panel. A large helicopter fuselage fragment was also found Thursday night near Irabu Island. In addition, media reported that rescuers found what are believed to be several bodies of the helicopter's crew near Irabu Island.
The helicopter underwent a special inspection in late March after 50 flight hours and was taken for a one-hour flight to check its safety, but no abnormalities were found at that time, the GSDF officials said.
Eight of the 10 people on board were high-ranking military officers, including the commander of the GSDF's 8th division, Yuichi Sakamoto, who was appointed to the post on March 31.