The girl, who belongs to Shahjahanpur, UP, was studying in class 12 while her brother was in class 8 at the gurukul in Chhindwara, 250 km southeast of Bhopal.
Chhindwara additional superintendent of police Neeraj Soni said the girl's father came with the team.
Meanwhile, Asaram Bapu in Indore denied the rape charge and said, "She is like my granddaughter, daughter and niece."
He said he would not seek anticipatory bail but was not averse of using legal aid. "This complaint does not stand a chance as it has been cooked up by some elements. They misguided our own sadhaks (followers) and lodged a fictitious complaint against me."
He, however, refused to comment whether any political party was behind this.