The 52-year-old man, who cannot be named to protect the identity of his alleged victims, appeared in Rockhampton Magistrates Court on Friday.
Police prosecutor Sergeant Joe Aboud said the daughter of the defendant's partner complained of the rape in 2010 when she was 15, but her mother did not believe her.
The man's partner told police she and the man were recently babysitting a nine-year-old girl when she left him alone in the room.
Sgt Aboud said when the woman returned she found the defendant rubbing the child's chest and she and the man argued.
During the argument, Sgt Aboud said the 2010 alleged rape of her daughter came up and he told the woman he didn't hurt the girl, but he did touch her sexually.
The accused allegedly told the woman her daughter could have stopped it.
Sgt Aboud said the man also asked the woman how to "knock out" the nine-year-old so he could sexually abuse her.
The man did not enter a plea and Sgt Aboud opposed bail on the basis the man might contact the victims and jeopardise the investigation.
Magistrate Tom Bradshaw refused bail and remanded the man in custody until April 18.