As per the complaint lodged by the victim's family, the nine-year-old girl, a student of 4th standard in a mission school, was raped on September 5 in the school hostel by her principal in connivance with the warden and caretaker, police said.
The accused were pressurising her against disclosing the matter to anyone and the hostel administration also tried to hush up the matter, they said.
The girl's health was deteriorating, but somehow she managed to inform her family about the incident, with the help of the hostel security guard, they said.
After receiving the complaint, a case was registered under relevant sections of the IPC and the Protection of Children from Sexual Offences (POCSO) Act, they said, adding the three accused were arrested.
Meanwhile, local residents alleged that the police tried to hush the matter up and took action only after the intervention of senior officials.
Further investigation is on, police said.