Lt. Rick Chernitzer said officials examined the USS Chancellorsville on Monday, a day after it pulled into San Diego.
The ship was tracking the unmanned aircraft during radar testing Saturday off Point Mugu in Ventura County when it struck the Chancellorsville.
Two sailors were treated for minor burns.
Officials declined to comment further while the cause is being investigated.
The aerial drone was a BQM-74 series, manufactured by Aerospace giant Northrop Grumman Corp. According to the company website, the drones can simulate enemy missiles or airplanes.