A bench headed by CJI asked the petitioner to approach the high court.
Additional director health Pushkar Anand said these fresh deaths occurred between August 12 and 14.
Two children succumbed to encephalitis in Gorakhpour, taking the toll in the viral disease in eastern Uttar Pradesh to 101 this year.
The hospital superintendent has blamed malnutrition for the deaths.
Overall, since January 1, as many as 144 encephalitis-related deaths have taken place in the hospital, they said.
As many as 16 children have succumbed to encephalitis in Gorakhpur district, Uttar Pradesh in the past 24 hours, taking the death toll in eastern Uttar Pradesh to 495.
There have been 1,256 deaths since January this year at the hospital, the principal said.
Khan, who was the nodal officer at the state-run hospital's paediatric department, had been hailed as a hero after he reportedly bought oxygen cylinders with his own money during the crisis.
The BJP president dismissed the Congress's demand for resignation of Uttar Pradesh Chief Minister Yogi Adityanath over the death of several children in a Gorakhpur hospital, saying such tragedies had happened during that party's rule also.
Dr Bhupendra Sharma will now take over as the nodal officer of pediatric department.
However, chief medical officer Dr Ravindra Kumar, part of the panel, said that the deaths were not due to lack of oxygen.
'...and the government is suppressing the truth.'
As many as 11 children died on Saturday and until Friday the death toll stood at 60.
Tandon also assured of a high level probe into the multiple deaths, headed by the principal secretary. An action will be taken after a due report is taken out.
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