Maj. Gen. Michael T. Harrison, a 33-year veteran of the Army, will be replaced by Maj. Gen. James C. Boozer until the investigation is completed, the Los Angeles Times reported Friday.
No details about the alleged assault were provided.
Harrison, who has commanded the Army contingent since 2010, was due to be transferred to U.S. Central Command in Kuwait, where he was to be deputy commander of the Army contingent there.
In a separate announcement, the Air Force said Maj. Gen. Margaret H. Woodward would head up its office of sexual assault prevention. She replaces Lt. Col. Jeffrey Krusinski, who was relieved of duty after being arrested in May on charges of groping a woman.