The proprietors of M/s Pushpa Sales, the company responsible for the supply of liquid oxygen, have also been named in the FIR.
Besides, the state government has transferred Additional Chief Secretary (Medical Education) Anita Bhatnagar Jain in connection with the tragedy, an official spokesperson said.
A probe committee, headed by the state chief secretary, had yesterday submitted its report on the deaths to Chief Minister Yogi Adityanath.
"An FIR has been filed against nine persons including former principal Dr Rajiv Mishra, his wife Dr Purnima Shukla, Dr Kafeel Khan and the proprietors of M/s Pushpa Sales," Additional Director General (Lucknow Zone) Abhay Prasad told PTI.
The FIR was filed under various IPC sections relating to criminal conspiracy and culpable homicide and relevant provisions of the Anti Corruption Act by Director General, Medical Education, KK Gupta at the Hazratganj police sation here, the ADG said.
The case has been transferred to Gorakhpur, he said.
The probe committee had recommended initiating criminal action against the then principal of the medical college, HoD Anaesthesia Paediatric department Dr Satish, in-charge of 100 -bed AES ward Dr Kafeel Khan and M/s Pushpa Sales.
It had also called for a special CAG audit of the medicines and chemicals purchased by the medical college in the past three years.
Recommendations were also made to initiate criminal action against Dr Khan for concealing facts and filing false affidavit and working against the rules of the Indian Medical Council.
The chief minister, while accepting the report, had ordered immediate action against all the guilty officials and staff.
Chief Minister Adityanath had formed the committee on August 12, a day after the deaths of children were reported at the hospital.
The state government has also shunted out additional chief secretary medical education Anita Bhatnagar Jain.
Rajneesh Dubey, who is presently principal secretary revenue, would be holding the additional charge of the medical education department.