Court documents said a report was filed against 40-year-old Aaron Walker in August 2013 stating the sexual misconduct happened at a Lexington hotel.
Walker is a drill sergeant and non-commissioned officer at Fort Knox.
Walker was interviewed by police and denied the abuse, according to documents.
Following the interview with police, Walker reportedly went to a sergeant at Fort Knox and admitted he abused the girl but said that the abuse took place on the base, where he had a room.
Police spoke with Walker again, who confessed, according to court documents, but twice changed the location where the abuse took place.
An officer said records were checked at the Lexington hotel where the girl said the abuse happened.
According to documents, Walker and the child did check into the room on the date of the alleged abuse.
Walker is charged with sexual abuse.