Parents accused health authorities in Gorakhpur city of trying to cover up their failure to pay bills on time to a firm that supplied oxygen cylinders.
The clinic caters to large parts of Uttar Pradesh (northern region) and Bihar (north and eastern region) states, a region known for encephalitis, a monsoon season disease that largely affects the young, poor and malnourished.
By Saturday, 63 infants were reported to have died at the Baba Raghav Das (BRD) clinic.
The Uttar Pradesh state government has suspended the hospital head following the children's deaths, with state health minister on Sunday vowing to act against the culprits.
On Sunday, J.P. Nadda, health minister in PM Narendra Modi's cabinet, visited the hospital along with the state's Chief Minister, Yogi Adityanath.
Anger and anguish
But the angry parents are not satisfied with the government's actions, and opposition parties are demanding Adityanath's resignation.
Adityanath said he had ordered a probe into potential lapses, including the role of the oxygen supplier.
State Health Minister Sidharth Nath Singh said the BRD also cared for neighboring states and over the past three years had an average of between 19 and 22 child deaths daily in August.
"The figures have to be taken into perspective," Singh said.
Opposition political leaders visited Gorakhpur on Saturday and blamed the governing BJP party of Prime Minister Narendra Modi.
Parents and adult relatives, who had accompanied ailing children on Thursday, said they were given self-inflating bags, normally used for accidents, to help their children breath.
"We saw our baby struggling to breathe and we couldn't do anything," said Parmatma Gautam, whose 1-month-old nephew, Roshan, died.
"We are now going back with his body," Gautam sobbed.
"Doctors told us no ventilator was available," bereaved parent Srikrishan Gupta told NDTV broadcasting.
"I used the manual resuscitator for about five hours," Gupta said, referring to his 4-day-old son who was in the clinic's neo-natal intensive care unit.
"There was chaos in the ward, children were not being treated properly," he said.
Another father, Mritunjaya Singh, whose son was not among those who died, said the oxygen supply to the children's ward ran out on Thursday night.
"That's the time when the death[s] of the children peaked," Singh said.
Cases of encephalitis
A doctor leading the campaign against encephalitis, R.N. Singh, said, "The government needs to tackle it with a rigorous campaign."
"Commonly, this disease affects the voiceless poor, so it has not got the attention it warrants," Singh said.
Encephalitis had a mortality rate as high as 30 percent, Singh said.
Hospital spokesman Satish Chandra said the clinic had treated nearly 370 cases of encephalitis in the past two months. Of these, 129 children had died.
ipj/sms (AP, dpa, AFP)