The accused preacher has been identified as Vasudeo Shastri, a resident of Lohari town in Maharashtra's Beed district, they said.
Shastri had brought the two girls to Vrindavan three-four months ago from his hometown on the pretext of imparting them education on religious scriptures, the police said.
He was living in a rented accommodation in Motijheel area of Vrindavan for the last four years. The matter came to light when the girls recently alerted their parents back home about their ordeal and they arrived here, a police official said.
An FIR has been lodged and Shastri booked for rape and criminal intimidation, he said.
He added that the girls have been sent for medical examination while the accused will be produced before the magistrate tomorrow.
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