The girl, who has lost her mother and whose father is in jail, lives in a shelter-house for children here.
City superintendent of police Indrajeet Bakalwar said the main accused was a 12 years old boy, a class sixth student of the same school where the girl was studying in the kindergarten.
Police suspected that two others were also involved, and all three were identified but nobody had been arrested yet, he said.
"The girl told a woman superintendent about feeling pain when she returned from the school yesterday evening. Then an FIR was lodged with Vijay Nagar police station," he said.
The accused allegedly raped the child in the school's bathroom. Medical examination confirmed the rape, police said, adding that further investigation was on.
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