According to sub inspector Pratap Pawar of Mumbra police station, the duo were studying in Almas Colony Jalmia Islamia Noorbaugh Madrasa.
Police suspect both Mohamad Yasim Mosim and Mohamad Dhanish Ansari were abducted and searches are on to trace them.
The Madarsa chief Sarfaraj Ramjanali Shamini, after conducting a search since October 29 morning, filed a police complaint yesterday.
Offences have been registered under section 363 of IPC.