On Monday, seven sailors were injured when an F-35 slammed into the flight deck and fell into the water on the USS Carl Vinson.
Deputy Public Affairs Officer Lt. Mark Langford said the pilot was able to eject safely after suffering a "landing mishap" during routine flight operations in the South China Sea.
The pilot was recovered by a helicopter.
The pilot and two other sailors were flown to a treatment center in Manila, Philippines, where they are "stable," the military said.
The Navy said four others were treated on the aircraft carrier by medical personnel, three of whom have been released.
Langford said the impact to the flight deck was "superficial" and the ship was able to resume its routine flight operations.