Weemer was a rifleman in a four-man team when ground forces entered Falluja and faced heavy fighting, often engaging in hand-to-hand combat.
The authorities say his involvement came to light during a lie-detector test when he was applying for a job with the Secret Service protective agency after he completed active duty in the military.
Investigators say Weemer described the killing during a polygraph lie-detector test that included a question about whether he had participated in a wrongful death.
Weemer, who remained a marine reserve, was reactivated this week, paving the way for him to be court-martialled.
Another marine from Weemer's unit, Sergeant Jermaine Nelson, was charged with murder last year in connection with the death of a detainee.
A third soldier, Jose Nazario, is being tried in civilian courts in California on manslaughter charges in connection with the shooting deaths of two Iraqi prisoners.
Nazario, who denies the charges, is awaiting trial.