None have been publicly identified and a search for two other crew members and the aircraft continues.
The defence ministry spokesman who confirmed the discovery had no other details, but media reports said that metal fragments were also found in the search area in southwestern Japan.
The U-125 aircraft left a military base in Kagoshima prefecture on the island of Kyushu this afternoon and later "disappeared from radar", officials said.
About 600 rescuers, including troops and fire fighters, resumed searching for the plane in mountainous terrain near the base early today.
Public broadcaster NHK has showed footage of helicopters searching forest-covered mountains for the aircraft.