"Asaram denied the charges and said he is innocent," Joseph told reporters in Jodhpur city, over 350 km from here.
Police officials said a Rajasthan court had given them Asaram's one-day remand for questioning.
The police chief said Asaram had undergone a medical examination and the doctors had declared he was fine.
"We would recreate the crime scene during investigation and the accused would be taken to the place of incident," said Joseph.
Earlier, a Rajasthan Police team flew Asaram Bapu, 72, to Jodhpur city in the afternoon after arresting him past midnight Saturday from his ashram in Indore in Madhya Pradesh.
The girl lodged a complaint Aug 20, accusing Asaram of sexually assaulting her at his ashram in Jodhpur. Asaram has denied the charge, and his son has claimed the girl was "mentally unstable".
Asaram has been booked under various sections of the Protection of Children from Sexual Offences Act and the Indian Penal Code.
According to the allegations of the girl, who studied at Asaram's ashram in Madhya Pradesh's Chhindwara and stayed in a girls' hostel there, the guru sexually assaulted her on the pretext of exorcism.