Miami-based US Southern Command said Army Capt. James Yee had been charged with two violations of the Uniform Code of Military Justice for failing to obey a lawful general order.
Specifically, Yee is accused of taking classified material to his home and wrongfully transporting the material without proper security containers or covers.
Yee, 35, was arrested on 10 September at Jacksonville Naval Air Station in Florida as he arrived back in the United States from Guantanamo, Cuba. Until Friday he had been held without charges at a military prison in Charleston, South Carolina.
More charges may follow
A defence official, speaking on condition of anonymity, described the charges as "preliminary" and necessary to keep holding Yee, but said the Army continues to investigate him and additional charges may be filed.
Conviction on each charge of failing to obey an order carries up to two years in prison, dishonourable discharge and forfeiture of pay, officials said.
Yee is one of three men arrested in an espionage investigation relating to Camp X-ray in Guantanamo, where the US military is holding about 660 foreign terrorism suspects from 42 countries, most captured in Afghanistan, without charges or legal representation.
The other two arrested were Arabic-language translators.
Ahmad Mehalba, a naturalized US citizen of Egyptian descent who worked as a civilian contractor, was arrested last week in Boston and charged with lying to federal officials about apparently classified information he was carrying.
"We had sufficient evidence that (Yee) had violated the procedures in place for classified material given what he had in his possession"
Air Force Master Sgt. Jose Ruiz,
Southern Command spokesman
Air Force Senior Airman Ahmad al Halabi, a naturalized US citizen of Syrian descent, was arrested on 23 July in Florida and charged with spying for Syria and aiding the enemy.
The arrests have triggered an investigation into security lapses at the Camp Delta prison facility at Guantanamo, but officials have said they do not know if there was a coordinated attempt to infiltrate the base.
"We had sufficient evidence that (Yee) had violated the procedures in place for classified material given what he had in his possession," said Air Force Master Sgt. Jose Ruiz, a Southern Command spokesman.
Yee, who also uses the first name Yusuf, is a 1990 graduate of the US Military Academy at West Point, New York. Raised a Lutheran in New Jersey, the Chinese American converted to Islam while in the Army at about the time he served in Saudi Arabia after the 1991 Gulf War.
Yee resigned his commission and spent four years studying Islam in the Syrian capital Damascus, then rejoined the American military as a Muslim cleric. He ministered to many of the prisoners at Guantanamo during 10 months of duty.
Southern Command did not identify the classified material Yee was accused of possessing, but officials have said he had maps and diagrams of the prison facility.
Southern Command said the charges against Yee have been forwarded to Maj. Gen. Geoffrey Miller, the commander of the military joint task force running the prison.
Miller had the option of referring them to a court-martial, convening an Article 32 hearing, which is the military equivalent of a grand jury proceeding, or dismissing the charges. The timing of any proceedings has not been determined.