Don M. Ayala, 46, of New Orleans was charged with second-degree murder in U.S. District Court in Alexandria. The U.S. Attorney's Office said Thursday that Ayala is in Afghanistan awaiting transfer to Virginia.
It is the first case in which federal prosecutors have brought murder charges against a military contractor serving in Iraq or Afghanistan under the 2000 law that allows such prosecutions, according to the Justice Department.
Messages left Thursday for Ayala's attorney, John Tranberg, were not immediately returned.
According to an affidavit, Ayala worked for contractor BAE Systems as security for what the Army calls a Human Terrain Team, in which social scientists and anthropologists are embedded with combat brigades to help soldiers understand local culture.
On Nov. 4, Ayala was on patrol about 50 miles west of Kandahar when an Afghan civilian named Abdul Salam ignited a pitcher of fuel and threw it on social scientist Paula Loyd, according to the affidavit.
Ayala helped subdue and arrest Salam, who was restrained and placed in plastic handcuffs, according to the affidavit.
About 10 minutes later, after a soldier said Loyd had been badly burned, Ayala pointed a pistol at Salam's head and shot him dead, according to court records.
Loyd had second- and third-degree burns over 60 percent of her body, according to the affidavit.
Before working for BAE systems, Ayala was a contractor providing personal security to both Afghanistan's president and Iraq's prime minister, according to the affidavit.
Ayala is charged under the Military Extraterritorial Jurisdiction Act (MEJA), a 2000 law that allows the prosecution of civilian contractors who commit crimes while working for the U.S. overseas. The U.S. Attorney in Alexandria has overseen a number of MEJA prosecutions.
Critics have said the Justice Department has been reticent to prosecute contractor misconduct.
While the Ayala prosecution is the first murder case under MEJA involving a military contractor, there have been similar cases against nonmilitary contractors.
In 2007, CIA contractor David Passaro was sentenced to more than eight years in prison after being convicted of assault for beating an Afghani detainee who later died. A former soldier, Steven Dale Green, is facing murder and aggravated sexual assault charges in federal court in Kentucky for allegedly raping an Iraqi teenager in 2006 and shooting and killing her family.
Prosecutors are also reviewing possible charges against employees of State Department contractor Blackwater Worldwide for their role in the shooting deaths of 17 Iraqi civilians last year.
BAE Systems Inc., based in Rockville, Md., is the U.S. subsidiary of London-based BAE Systems plc. A company spokesman did not return calls seeking comment Thursday.