In 2006, Congress gave the military authority to prosecute crimes allegedly committed by civilians working for the armed forces.
Lt. Gen. Lloyd J. Austin III, the second-ranking U.S. commander in Iraq, referred the case, the military said in a statement.
"This is the first time a civilian will be tried by court-martial" under the 2006 amendment, it said.
Sunday's statement said Ali "is being afforded all the same rights, protections and privileges service members receive in military court, including the right to counsel, right to speedy trial, protection against self-incrimination and presumption of innocence."
Ali was being represented by military defense counsel, it added.
During the war in Vietnam, several civilians working for the U.S. armed forces were charged with violations of military law. Although there were several convictions, they eventually were struck down by the U.S. Supreme Court.
