Brigadier General Jeffrey Sinclair, who is based at North Carolina's Fort Bragg, has also been charged with wrongful sexual conduct, misusing a government travel charge card, possessing alcohol and pornography while deployed and mistreating subordinates, military officials said in a statement.
Sinclair, a 27-year Army veteran, had served as a deputy commander for support in Afghanistan. At least some of the allegations involved inappropriate relationships with female subordinates during his service there, said a US official speaking on condition of anonymity.
Two US officials said Sinclair was sent home in May over the allegations.
A hearing will be held to determine whether the case should be referred to a court-martial, said Colonel Kevin Arata, a Fort Bragg spokesman. No date has been set.
"The purpose of the hearing is to determine the merits and seriousness of the charges so as to make recommendations on whether the matter should proceed to trial or not," Colonel Arata said at a news conference on Wednesday.
"Given the nature of these proceedings, it would be inappropriate to comment any further at this time," he said.
According to a biography of Sinclair provided by the Army, he has served combat deployments in Saudi Arabia, Iraq and Afghanistan, and has received a host of awards and decorations during his service.