TEHRAN, Young Journalists Club (YJC) - Eight other people were rescued and transferred to the carrier where they were in good condition, the U.S. Seventh Fleet said.
"Search and rescue efforts for three personnel continue with U.S. Navy and Japan Maritime Self-Defense Force (JMSDF) ships and aircraft on scene," the U.S. Seventh Fleet said in a news release.
"The incident will be investigated," it added.
The plane was conducting a routine transport flight carrying passengers and cargo from Marine Corps Air Station Iwakuni to the carrier, which was operating in the Philippine Sea as part of an exercise with Japanese forces, it said.
U.S. President Donald Trump was briefed on the crash at his Mar-a-Lago retreat in Florida, where he is spending the U.S. Thanksgiving holiday, said White House spokeswoman Lindsay Walters.
"The @USNavy is conducting search and rescue following aircraft crash. We are monitoring the situation. Prayers for all involved," Trump wrote in a Twitter post.
Japanese Minister of Defence Itsunori Onodera told reporters the U.S. Navy informed him that the crash may have been a result of engine trouble.
The propeller-powered transport plane, a C-2 Greyhound, carries personnel, mail and other cargo from mainland bases to carriers operating at sea.
C-2 aircraft have been in operation for more than five decades and are due to be replaced by the long-range tilt-rotor Osprey aircraft.
Two crashes in the Asia Pacific region involving U.S. Navy warships and commercial vessels this year have raised questions about Navy training and the pace of operations in the region, prompted a Congressional hearing and the removal of a number of officers.
The guided missile destroyer Fitzgerald almost sank off the coast of Japan after colliding with a Philippine container ship on June 17. The bodies of seven U.S. sailors were found in a flooded berthing area after that collision.
In a separate incident in August, 10 sailors were killed when the guided missile destroyer John S. McCain collided with an oil tanker.
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.