The 49 children died in the last one month and the FIR was registered last night by the city magistrate, the sources said.
After local channels reported the death of 49 children in the hospital, Chief Minister Yogi Adityanath's office took cognisance of the matter and directed District Magistrate Ravindra Kumar to conduct a probe.
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The FIR was registered against the COM and CMOS for their alleged laxity, he said.
City Magistrate, Jayendra Kumar Jain and SDM Ajit Kumar Singh said the probe found that deaths were due to lack of oxygen.
The death of children in the Farrukhabad hospital comes after at least 30 children died in a state-run hospital in Gorakhpur on August 10-11 amid allegations of oxygen shortage.
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