The 12-year-old girl was sexually assaulted by Piyush, younger son of the school manager Chanderpal Verma, the team claimed in its report that is being sent to authorities in Lucknow.
The report also accused Verma and his elder son Mukesh for not taking the victim to the hospital on time following which the girl died.
A chargesheet will be filed in the case soon, the CB-CID officials said. They also said that a neighbour of the girl, Munna, who was arrested by the police, is not involved in the case and will be soon released from jail.
Fourteen DNA samples, included that of Chanderpal Verma, Mukesh, Piyush, Munna, were taken in connection with the case, CB-CID ASP D P Srivastav and Investigating Officer Arun Kumar told PTI.
The samples were sent for testing at forensic laboratory in Lucknow and Hyderabad, they said.
According to preliminary investigations, the CB-CID team found that the 70-year-old school manager was at his home, while his elder son was in Unnao at the time of the incident.
Piyush was, however, near the school premises, they alleged and claimed that call details of Piyush's mobile phone also helped in establishing his involvement, they said.
Piyush, who is the main accused, will be booked under IPC 377 (unnatural offences) in the chargesheet to be filed by the team on January 3, they said.
Meanwhile, Kanpur DIG Ashok Mutha Jain said since the matter was being probed by CB-CID, the team will submit their report to officials in Lucknow.
On September 27, the 12-year-old student was allegedly sexually assaulted at Bharatiya Gyan Sthali School. The girl was sent back home along with two maids and her mother was informed at her work place.
The girl was admitted to a hospital where she died the same day. Verma, along with his son Mukesh were later arrested under section 109 (punishment for abetment) and 304 (A) (causing death by negligence) of the IPC. Later, Verma's younger son Piyush was also arrested.
On October 23, the Uttar Pradesh government ordered the CB-CID probe into the case.