The Ronald Reagan was leading the search and rescue efforts, which included three US destroyers as well as helicopters and surveillance aircraft.
A spokesman quoted Defense Minister Itsunori Onodera as telling reporters Wednesday that the C-2 aircraft crashed into the Pacific about 150 kilometers (90 miles) northwest of Okinotorishima, a Japanese atoll.
A U.S. Navy transport plane carrying 11 people crashed in the Philippine Sea south of Japan on Wednesday as it flew to the aircraft carrier Ronald Reagan and three people were missing, in the latest Navy accident in the region.
But unfortunately, the aircraft crashed almost 500 nautical miles at the southeast of Okinawa, Japan.
It says that preliminary USA military reports indicated that engine failure may have caused the crash.
Their C-2 "Greyhound" transport plane crashed while on its way to the carrier on Wednesday in the Philippine Sea, where the USA and Japanese navies are holding exercises.
The search, which had covered more than 320 nautical miles by Thursday morning, was being aided by three destroyers and two helicopter carriers from the Japan Maritime Self Defense Force. The bodies of seven USA sailors were found in a flooded berthing area after that collision.
The C2-A that crashed Wednesday belongs to a Japan-based squadron that generally flies cargo and passengers between shore bases and the USS Ronald Reagan.
The Japan-based 7th Fleet says in a statement that the search and rescue operation has been launched from the carrier.
President Donald Trump tweeted that the US Navy is monitoring the situation.
In August, Vice Adm. Joseph Aucoin was relieved of his duty as the commander of 7th Fleet following a deadly collision between the destroyer USS John S. McCain and a merchant ship off Singapore that left 10 USA sailors dead.
In June, the USS Fitzgerald collided with a cargo ship off Japan, resulting in the deaths of seven USA sailors.
The Navy has dismissed a number of officers, including the commander of the Seventh Fleet, as a result of the collisions involving its warships in Asia.
In January, the guided missile ship USS Antietam ran aground in Tokyo Bay.