The incident took place on January 2 when the teacher, identified as Abdul Latif, thrashed eight-year-old Mohammad Siraj badly with sticks after removing his clothes, police said.
According to the FIR filed on the complaint of Siraj's father, the minor, who was staying in the madarssa was allegedly held captive there by Latif for two days without any food.
The matter came to light on January 4 when the father, Najim Ali, went to the madrassa to take him home, SHO Brijest Pandey said.
Police has launched a manhunt to nab the accused, who is absconding.