On the night of the alleged attack the driver had returned back to the villa intoxicated after watching a soccer match, the ABC reported.
When walking past the girl's room and noticing she was asleep, he then turned off the outdoor light, picked her up and carried her to a neighbouring plot of land, police allege.
Deputy Commissioner Putra told the ABC that the nine-year-old initially thought it was her father.
It was only when the man allegedly began taking off her pants and molesting her that she began to scream.
The girl's screams alerted people nearby, the Seven Network reported on Thursday.
The network said a 33-year-old man has been arrested and charged.
It is believed the girl noticed the man's pontytail and picked him out of a line-up of suspects, the ABC reported.
The girl's family, believed to be from the Byron Bay area in northern NSW, remains in Bali.
-AAP