The 16-year-old boy, a school dropout, has been arrested and remanded to custody in a government observation home today, they said.
The girl, a class II student of Thelunganur off nearby Mettur, went missing on July 2 evening after she went out to play and her father Raja, a fisherman, lodged a complaint with police yesterday.
During investigation, police was told by locals and friends of the missing girl that the victim was led away by a boy of the same area.
He allegedly confessed that he raped, assaulted and killed the girl by strangulating her.
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"He was produced before the District Juvenile Justice Board today which remanded him to custody till July 18 in a Government Observation Home here," Kolathur Police Inspector S Viswanathan said.
"Case for offences under several IPC sections including trying to destroy evidence has been registered against the accused. We have also invoked the POCSO (Protection of Children from Sexual Offences) Act," he told PTI.