The peon allegedly sexually assaulted the girl inside a washroom of the school between August 1 and 4, Senior police Inspector of Dindoshi police station, Rajaram Vhanmane said.
Her mother filed a complaint on August 5.
A case on the charge of rape and under relevant sections of the Protection of Children from Sexual Offences Act was registered, said the officer.
"We subsequently identified and apprehended the accused yesterday (Monday)," Vhanmane said, adding the accused was produced in a local court which remanded him in police custody till August 11.
On Tuesday morning, parents of other students gathered outside the school and staged a protest.
"The parents want assurance of safety of their children," Deputy Commissioner of Police (Zone-12) Vinay Rathod said.
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