The JMO has recommended that the badly decomposed body be referred to a forensic expert and report obtained to determine the circumstances that had led to her death.
Udayakumar Yarshika went missing on June 21 while taking a bath with her family.
A team of around 400, comprising police, Navy and STF as well as villagers searched for her for five days, but they failed to find any clue.
Acting on a tip-off, police found the girl’s body from a paddy field on July 19.
It is believed she had been killed elsewhere and the body dumped at the paddy field.
Four suspects, including the alleged rapist, a 14-year-old, was arrested on June 27 and remanded for questioning, said police spokesman ASP Ruwan Gunasekara.
The youth has confessed to having raped Yarshika and strangled her for fear of disclosure, BBC Sandeshaya reports.