The victim was allegedly sexually assaulted on December 8, police said, adding that her elder brother from Daanramuda village had lodged an FIR in this connection belatedly.
Manoj Mallick (32), a truck driver who had criminal antecedents, has been taken into custody. The accused hailed from the same village as that of the victim.
The accused, who had acquaintance with the girl, coercively sexually assaulted her.
"The offender has confessed to the crime," said Kendrapara Superintendent of Police Rabi Narayan Behera.
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The girl was medically examined and her statement has been recorded. There was corroborative evidence of sexual assault on the minor girl, said the SP.
The accused had fled after committing the crime. He was apprehended from a nearby village by a special squad constituted for the purpose, he said.
The accused has been booked under Indian Penal Code Section 376 (Rape), Section 557 (Assault or criminal force in attempt wrongfully to confine a person), Section 342 (wrongful confinement), Section 506 (criminal intimidation) and Sections 4 and 6 of Protection of Children from Sexual Offence Act, 2012.