The hospital superintendent has blamed malnutrition for the deaths.
Additional director health Pushkar Anand said these fresh deaths occurred between August 12 and 14.
A bench headed by CJI asked the petitioner to approach the high court.
Overall, since January 1, as many as 144 encephalitis-related deaths have taken place in the hospital, they said.
Two children succumbed to encephalitis in Gorakhpour, taking the toll in the viral disease in eastern Uttar Pradesh to 101 this year.
There have been 1,256 deaths since January this year at the hospital, the principal 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.
Dr Bhupendra Sharma will now take over as the nodal officer of pediatric department.
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.
With the fresh arrest, all the nine persons named in the FIR have been sent to custody.
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.
However, chief medical officer Dr Ravindra Kumar, part of the panel, said that the deaths were not due to lack of oxygen.
As many as 11 children died on Saturday and until Friday the death toll stood at 60.
This is the third arrest made by the STF in the case.
Prime Minister Narendra Modi on Tuesday mentioned in his Independence Day speech the recent death of nearly 70 children at a state-run hospital in Uttar Pradesh, and said sympathies of the entire nation were with the affected families.
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.
'...and the government is suppressing the truth.'
Kafeel Khan's mother has demanded police protection for her family.
Police said the teacher has been arrested under Section 306 of the Indian Penal Code.
If any party gives me a ticket I am ready, Khan said .
Dr Kafeel Khan and 80 others have been included in the list of history-sheeters in Gorakhpur district of Uttar Pradesh and they will be on the radar of police, officials said.
Seventeen children died in the neo-natal ward, five in the acute encephalitis syndrome ward and eight in the general ward.
A bench headed by Chief Justice S A Bobde, which was hearing the Uttar Pradesh government's plea challenging the high court's September 1 verdict, said it is 'a good judgment'.
The infants had died allegedly because of disruption in oxygen supply due to pending payments to the supplier, a charge stoutly refuted by the state government.
Dr Kafeel Khan, whose name surfaced in the 2017 Gorakhpur encephalitis deaths case, has expressed gratitude to superstar Shah Rukh Khan for shedding light on the tragic incident through his blockbuster film Jawan.
The BJP is banking on development. The opposition is raking up caste identities and the dangers of hyper nationalism.
Khan has been in jail since January after he delivered the allegedly provocative speech at the AMU during the anti-Citizenship (Amendment) Act protests in December last year. He is lodged in Mathura jail.
