It was taking part in an ongoing joint U.S. -Japan naval exercise.
The government in Tokyo said it had been informed eight people had been plucked to safety, and that U.S. authorities had said engine trouble was the suspected cause of the accident.
The C2-A Greyhound aircraft was on a routine flight from Marine Corps Air Station Iwakuni in southern Japan to the USS Ronald Reagan aircraft carrier, which is now in the Philippine Sea on exercises with Japan's Maritime Self-Defense Force.
Navy officials said 8 people were rescued and in "good condition".
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U.S. and Japanese naval ships and aircraft are searching for the missing.
The cause of crash is unknown and the names those onboard are being withheld while next of kin are notified, the US Navy said in a statement.
Reports say U.S. military vessels has recently involved in several numbers of accidents in recent time in East Asia. Japan time (5.45 a.m. GMT).
The Navy's Japan-based 7th Fleet has had two fatal accidents in Asian waters this year, leaving 17 sailors dead and prompting the removal of eight top Navy officers from their posts, including the 7th Fleet commander.
Ten were killed when the USS John S. McCain collided with an oil tanker near Singapore in August, and seven died when the USS Fitzgerald ran into a much heavier container ship off the coast of Japan in June.