Santosh Rout, 45, was arrested after the girl's father lodged a complaint Friday.
The victim, a Class five student, had suffered injury marks on her body, a police officer said.
Rout allegedly dragged the girl to a secluded place and raped her Thursday evening when she had gone to fetch water from a tube well in Balikana village of Kendrapada district, about 170 km from here.
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