Master Sergeant John E. Hatley, 40, is charged with premeditated murder, conspiracy to commit premeditated murder and obstruction of justice, according to an army statement.
Hatley currently serves with the 172nd Infantry Brigade in Schweinfurt Bavaria, and is to face trial at the Rose Barracks Courthouse, near the town of Vilseck.
The charges are related to the killings of prisoners in March or April 2007 near Baghdad. An exact date has not been established and the bodies, which witnesses have said were pushed into a canal, were never found.
Two other non-commissioned officers - Sergeant Michael Leahy, a medic, and Sergeant First Class Joseph Mayo - have already been found guilty of taking part in the killings and sentenced to life and 35 years in prison, respectively. Both will eventually become eligible for parole.
Hatley's lawyer David Court told AFP last week his client would plead not guilty to the “unusual allegation of pre-meditated murder” and added, “The government has no evidence, they just have witness testimony.”
According to testimony from Mayo's trial, at which he pleaded guilty, all three sergeants shot the prisoners in the back of the head with nine-millimetre pistols.
Mayo, 27, said, “I really believed I was protecting my soldiers,” because he believed the men, who he said were captured in possession of assault rifles and a duffel bag full of ammunition, would mount attacks on US troops in the future.
Two sniper rifles were also found nearby and the US unit, which belonged to the 1st Battalion, 18th Infantry Regiment, then part of the 2nd Brigade of the 1st Infantry Division, had seen a sergeant killed by a sniper a few weeks earlier.
Mayo testified that Hatley had not forced either of the other two sergeants to shoot the detainees, and that a check with his unit found “they did not have an issue” with the decision.
The soldiers were posted at a combat outpost dubbed “Angry Dragon” on what one witness called a “fault line” between Shiite and Sunni fighters in West Rashid, one of the most violent Baghdad neighbourhoods at that time.
The exposed post was subject to repeated attacks but rules of engagement often resulted in prisoners being released after a few days, armed with updated intelligence on US methods.
That bred “frustration and fear”, according to Captain David Nelson-Fischer, a witness at Mayo's trial.
Nelson-Fischer also said in a statement read by a defence lawyer that US troops were unprepared for the explosive situation in which fighters from the Mahdi Army, a Shiite paramilitary group, were driving Sunnis from the area.
A total of seven US soldiers were implicated in the case, but only the three sergeants have been tried for murder.
Two soldiers have pleaded guilty to lesser charges and been sentenced to prison terms of less than a year, an army spokeswoman said.
Charges were dismissed against two others, including Staff Sergeant Jess Cunningham, who first revealed the killings to a lawyer in January 2008.