Sinclair was charged with the rapes just months after his sudden removal from his post in Afghanistan, NBC News reported.
Sinclair, a 27-year veteran of the Army, was relieved of his post in May. He also has been charged with possession of pornography and alcohol, and having inappropriate relationships with female subordinates while in country, NPR reported.
He faces an Article 32 hearing to determine if he should be court-martialed.
Only two generals have been court-martialed in the past 13 years, NBC said.