The boy, identified as Divyansh Kakrora, was a class I student at Ryan International School in Vasant Kunj, police said, adding he was last seen before the seventh period, which was around 12.20 PM.
The authorities then started looking for him and after sometime he was found floating inside the pit which is used as a water storage tank. It is under the ampitheatre in the school's playground.
An FIR has been registered at the Vasant Kunj North Police Station under Section 304 (A) of IPC against unknown persons for causing death due to negligence.
"Investigation of the matter is underway and whatever legal action needs to be taken, will be taken," DCP (South) Prem Nath said.
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Delhi Government has ordered a magisterial probe into the incident.
"We have ordered District Magistrate of New Delhi to probe the case. I need a report to take action. The probe will find facts and fix responsibility for the child's death," Deputy Chief Minister Manish Sisodia, who holds the Education portfolio, said.
The boy's father termed it a conspiracy and alleged that someone from the school authority was behind the incident.
Several police teams were rushed to the spot after the incident came to light. The school authorities were questioned and a case of negligence is likely to be registered in connection with the incident, a senior official said adding how he fell into the pit is still to be ascertained.