The incident took place Friday evening, said police inspector VC Dolas of Vitthalwadi police station.
He said a case under section 363 (kidnapping) of IPC has been registered in this regard following a complaint lodged by the hostel supervisor Uttam Sutar.
The boys are identified as Sachin Pawar (13), Pintu Munna Singh (11), Suaj Amar Mote (10) and Kailas Male (11).
In a separate incident, a case of kidnapping was registered against two teenagers after two sisters from Vitthalwadi went missing in wee hours yesterday, police said.
In another incident, a 15-year-old girl from Kalyan went missing on Friday evening.