The accused barged into the house of the victim after finding her alone and allegedly raped her, the official said.
The 3rd Metropolitan Magistrate, Warangal will cause a judicial enquiry and submit the enquiry report to the Registrar (Judicial), High Court, within four weeks, the HC said.
Labour Minister Ch Mallareddy on Tuesday kicked up yet another controversy by stating that the culprit would be shot dead in an 'encounter'.
The case was transferred from the Mayur Vihar police station to the Crime Branch on August 8.
The 400-page final report named Radhey Shyam, the 55-year-old priest of the crematorium in South-West district, and its employees, claiming there is sufficient evidence against them.
An official said that the incident took place on Friday afternoon when the nine-year-old boy was playing outside his house.
Standing counsel Sanjay Lao, appearing for State, said that an SIT has already been constituted after the case was transferred from the local police station to Crime Branch.
Nangal minor rape case: Accused tried to mislead probe, no sign of short circuit in cooler, says SIT
The investigation also revealed that the priest used to watch porn movies and get massage from the deceased girl.
The Congress questioned PM Narendra Modi's 'silence' on the alleged rape and murder of a 9-year-old Dalit girl in Delhi.
Dalit girl rape: No evidence to confirm if 9-yr-old violated before being killed, police tells court
Special Judge Ashutosh Kumar, meanwhile, awarded Rs 25 lakh as "interim relief" to the mother of the child for the loss of her daughter's life.
DCW chief Swati Maliwal lamented that there is no discussion on women’s safety in the country after the incident which happened in Trilokpuri.
A ministry spokesperson tweeted that the MHA reviewed the two incidents with Delhi Police officials, as per the directions of Union Home Minister Amit Shah.
Kejriwal had last week visited the parents of the victim and announced the compensation besides ordering a magisterial probe into the incident.
According to the prosecution, the minor girl was raped, murdered and then cremated without her parents' consent.
The visit comes a day after the case was transferred to Crime Branch for an expeditious and scientific investigation, they said.