The Washington Post quoted the US Navy's 7th Fleet, as saying, that eight people were found and the search for remaining three was underway.
However, it was not clear whether the people found were dead or alive.
The C-2 Greyhound aircraft was travelling to the USS Ronald Reagan aircraft carrier, which is currently operating in the Philippine Sea.
"The Maritime Self-Defense Force is currently searching with US forces," Onodera said, according to public broadcaster NHK.
He added, "We received information from U.S. Forces that the cause is possibly engine malfunction."
The accident is the latest in a series of disasters in 2017 for the 7th Fleet, including two collisions involving guided-missile destroyers that left 17 sailors dead. (ANI)