The accident happened during a training maneuver off the coast of San Diego.
The guided missile cruiser USS Chancellorsville was taking part in those drills when the drone plowed into the left side of the ship.
In a release Navy Lieutenant Lenaya Rotklein said "no person was seriously injured."
However, it was confirmed that two sailors were burned after the crash but their injuries are said to be minor.
The Navy is now left trying to figure out why the 13 foot long drone malfunctioned and plummeted into the ship during the during radar testing off Point Mugu in southern California.
The drone is said to be a BQM-74 series, produced by Northrop Grumman.
They are widely used in combat and weapons systems testing.
The company website says the unmanned craft are generally used to simulate enemy missiles or planes.
The Navy confirms the ship is in dock and repair assessments are being made.