The F/A-18 Super Hornet fell off the deck of the ship and was lost in the Red Sea, CBS News, NBC News and CNN reported.
The pilot and weapons systems officer were forced to eject from the aircraft following a failed arrestment.
They sustained minor injuries after they were recovered by a rescue helicopter, CNN reported.
A defense official told CBS News that no flight deck personnel were injured in the incident.
The cause of the incident was unclear but initial reporting, the tail hook failed to catch the wire that slows down the aircraft upon landing, and the jet then continued to accelerate toward the bow and over into the water, according to NBC News.
The first F/A-18E to fall into the water was being towed in the hangar bay in late April when the crew reportedly lost control of the aircraft, which led to both the jet and tow tractor to go overboard. U.S. officials said the jet may have fallen after the Truman turned while taking evasive action against Yemen's Houthi militants.
The Navy said the incident is under investigation. A single F/A-18E costs around $66 million to produce.
The Truman has seen other problems over the past year. It collided with a merchant ship in the Mediterranean Sea near the Suez Canal in February, which led to the removal of its captain. One of the Truman's F/A-18 fighter jets was mistakenly fired upon by another American aircraft carrier in December.
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