The incident was reported yesterday and the 22-year-old accused, a sweeper, has been arrested, police said.
The minor girl had gone to the washroom and sought help, but instead of a woman staff a male staffer came and allegedly sexually assaulted her, the police said.
After she reached home, she narrated her ordeal to her parents who informed the school and subsequently, the police were informed.
A case was registered and the accused, a resident of Dakshinpuri here, was arrested.
Also last month, a five-year-old girl was allegedly raped by a peon inside the premises of a private school in Shahdara here. The accused was arrested the same day.
Following the Shahdara rape incident, Delhi Police commissioner Amulya Patnaik had instructed all district Deputy Commissioners of Police to ensure that schools in their areas have adequate security measures in place.
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