CBI spokesperson Abhishek Dayal said the agency took over the probe after a notification from the central government was received on Friday.
According to the procedure, it has re-registered the FIR of the Gurugram Police which had been probing the matter.
“The CBI took over the investigation into the said case which was registered... at Bhondsi police station in Gurugram under sections 302 (murder) of the IPC, 25 of the Arms Act, 12 of the Protection of Children from Sexual Offences (POCSO) Act and 75 of the Juvenile Justice Act read with section 34 of IPC,” he said.
A CBI team also visited the office of the Gurgaon Police Commissioner late in the evening, sources said.
The Gurugram Police had arrested Ashok Kumar, one of the school’s bus conductors, in connection with the case.
On September 16, it had said the chargesheet had been prepared and Kumar was the only accused, but the SIT would not file it in court.
The report will be handed over to the CBI once it takes over the investigation within a couple of weeks, it had said.
Pradhyumn Thakur, a Class 2 student, was found dead with his throat slit in a toilet of the school on September 8.
Kumar was arrested the same day for allegedly killing the child.
Earlier in the day, Pradhyumn’s father Barun Thakur had told a press conference that he had appealed to the top leaders of the country to expedite the CBI inquiry into the “sensitive matter”.
Thakur’s lawyer alleged that the CBI inquiry had not yet started despite the Haryana government recommending it.
“If the formal inquiry by the CBI is not started by tomorrow, then Barun Thakur will move the Supreme Court on Monday” he added.
'Pradhyumn gives me the strength to fight'
Ryan murder: Post-mortem cites shock, haemorrhage as cause of death
How to ensure your child's safety at school
Ryan murder: State okays CBI probe; takes over school management
Ryan murder: Child couldn't cry for help due to slashed nerve