The accused Samiulla Karudddin Shah (25) had offered to teach the girls Arabic at the seminary which falls under Rabodi Police Station limits, they said.
He allegedly molested them at the madrasa, police said quoting the complaint filed by the father of one of the girls.
The girls (both aged 8) hailed from Rehmatnagar area, police said, adding Shah was apprehended last night and booked under section 354 (outraging modesty of woman) of IPC and under the Protection of Children from Sexual Offences Act 2012.
Meanwhile, in another incident, a BEST employee Laxman Chavan (50) from Kharigaon in Kalwa was arrested last night for allegedly molesting a six-year-old girl from the same locality, police said.
Chavan was booked under section 354 of IPC and the provisions of Protection of Children from Sexual Offences Act 2012, they added.