It would be the third known time a Patriot had failed to distinguish friendly from enemy targets in the war.
The Hornet was shot down as it was conducting a bombing run near Karbala, 50 miles south of Baghdad, on April 2. Lt. Nathan White, 30, of Mesa, Ariz., the pilot of the single-seat fighter jet, was killed, the Pentagon said.
At the time of the downing, there were conflicting reports about whether friendly or Iraqi fire was to blame. On Monday, Central Command said the Patriot battery had locked on the Hornet.
"Indications are that the F/A-18 went down as a result of being hit by a Patriot missile," said Capt. Frank Thorp, a Central Command spokesman. "An investigation is under way to determine why the Patriot missile battery engaged the F/A-18."
The military has equipment that's supposed to help, reports CBS News Correspondent Jim Acosta. Marines wear a special tape on their helmets that can be seen with night vision Goggles, and fighter jets have systems that can warn anti-aircraft weapons not to attack.
Such a system, however, did not spare one British fighter jet that was destroyed by a patriot missile, in the first friendly fire incident of the war.
In the March 23 incident, a U.S. Patriot missile battery fired on a British Royal Air Force Tornado GR4 aircraft as it was returning from a mission, killing its two crew members.
On March 25, an American F-16 fired on a U.S. Patriot missile battery south of Najaf after the battery's radar locked on the jet. The battery's radar was damaged.
In the April 2 incident, the Hornet was flying a bombing run from the aircraft carrier USS Kitty Hawk in the Persian Gulf when it was shot down during fierce fighting between U.S. troops and Iraqi Republican Guards. It became the first U.S. fighter jet downed in the war.
Since then, two other U.S. jets have been lost over Iraq.
An A-10 "Warthog" was shot down near Baghdad's airport April 8 by what Central Command believes was an Iraqi surface-to-air missile. The pilot ejected safely and was rescued by U.S. troops.
On April 7, an F-15E Strike Eagle fighter jet went down near Tikrit. There has been no word on the fate of the two crew.
U.S. Patriot missiles have intercepted more than 10 Iraqi missiles during the war, U.S. officials said.