Search and rescue efforts continue for the other three people on board the aircraft when it went down.
The crash, which took place about 500 nautical miles (575 miles) southeast of Okinawa, Japan, happened at 2:45 p.m. local time, which is 12:45 a.m. ET.
The USS Ronald Reagan is conducting search and rescue operations, the Navy said.
The cause of the crash is unknown.
The Navy said the C2-A aircraft was conducting "a routine transport flight carrying passengers and cargo from Marine Corps Air Station Iwakuni to USS Ronald Reagan."
The USS Ronald Reagan is currently operating in the Philippine Sea. The ship was taking part in Annual Exercise 2017 (AE17), a bilateral field-training exercise with the Japanese Navy conducted in waters off Japan from Nov. 16 to 26.
The accident is the latest in a series of disasters in 2017 for the 7th Fleet, which is stationed in Japan. In January, the USS Antietam ran aground off the coast of Japan, damaging its propellers and spilling oil into the water. The USS Lake Champlain collided with South Korean fishing boat on May 9.
Seven U.S. sailors were killed when the USS Fitzgerald collided with a Philippine-flagged container ship in the middle of the night off the coast of Yokosuuka on June 17.
And the deadliest accident came on Aug. 21, when 10 U.S. sailors were killed when the USS John S. McCain collided with commercial vessel Alnic MC in waters east of Singapore, according to the Navy.
The commander of the 7th Fleet was removed of his command in late August following the USS John S. McCain accident. Vice Adm. Joseph Aucoin was relieved of duty due to a "loss of confidence in his ability to command," according to the Navy.