Surendra Chowdhry, 57, allegedly tied the victim's hands behind her back with a handkerchief and then sexually assaulted her in western Sydney on New Year's Day in 2013.
Chowdhry also faces charges of indecently assaulting her three times during 2012 and twice again in January, the Sydney Morning Herald reported.
Child Abuse Squad officials arrested Chowdhry on Friday night. He wanted to "resolve the matters within the family", police told Parramatta Bail Court yesterday.
Police said the victim's father too expressed a desire to "bypass the police and judicial process".
The magistrate formally refused him bail and remanded him in custody.