The drone, which was being controlled from Point Mugu, was being used to check the USS Chancellorsville's radar-tracking system Saturday when it malfunctioned, the Los Angeles Times reported.
At about 1:25 p.m., the drone struck the side of the ship, causing some damage and injuring two sailors, CNN reported. Both sailors were treated for minor burns.
The ship, which has a crew of about 300 sailors, was returning to San Diego for inspection, the Navy said.
The Navy is investigating the cause of the malfunction.