The hospital recorded 49 deaths, 30 in neo-natal ICU and 19 during delivery, between July 20 and August 21, an official spokesperson said in Lucknow.
The state government today removed Farrukhabad District Magistrate Ravindra Kumar as well as Chief Medical Officer (CMO) Umakant Pandey and Chief Medical Superintendent (CMS) Akhilesh Agarwal.
An FIR against the CMO and the CMS was registered last night in Farrukhabad, about 180 km from the state capital.
"A high-level team will be sent to Farrukhabad to probe the deaths and its technical aspects will also be taken care of. Taking note of the incident, the DM, the CMO and the CMS (women's hospital) have been removed," the spokesperson said.
He said 468 deliveries took place in the women's wing of the hospital during the period. Of these, 19 were stillbirths.
City Magistrate Jaynendra Kumar Jain and SDM Ajit Kumar Singh said a probe found that most deaths were due to breathing problems. They also said in the report that the CMO and the CMS did not cooperate with the investigation.
"During the period, 30 children died mostly due to perinatal asphyxia (a condition in which a child does not breathe normally just before, during, or after birth). During probe, the parents informed that there was delay in providing oxygen and medicine due to which the children died due to lack of adquate supply of oxygen," the report stated.
The report did not mention the remaining 19 deaths.
Addressing a hurriedly convened press conference today, Principal Secretary (Health) Prashant Trivedi said the deaths had "nothing to do with oxygen supply".
"Stating that the deaths were related to oxygen amounts to making the matter unnecessarily sensational without any basis. the Director General Medical Health will give a detailed report on it," he added.
Principal Secretary (Information) Awanish Awasthi, who was also present, said, " 19 were still born children while 30 others died due to various causes, including perinatal asyphyxia. This may be caused by the umblical cord going around the neck of the child. Our medical team will look at it."
News of the deaths 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, a charge stoutly denied by the state government.