Though the government has denied oxygen shortage, parents and eyewitness accounts show how the situation spiraled out of control since Thursday.
Siddharth Nath Singh, the health minister of UP, said: "The death of children is very unfortunate and the government will set up an inquiry committee to ascertain if any lapse has occurred".
After the news of the incident broke out Gupta, who was the first to reaches at the Gorakhpur hospital, he said seven deaths were reported and most of these because of illness.
The Uttar Pradesh government has ordered an investigation.
"But the situation was managed through oxygen cylinders", Trivedi said.
Minister for medical education Ashutosh Tandon ruled out disruption in oxygen supply as the reason behind the deaths.
It is being said that oxygen supply was disrupted by the provider because of non-payment of dues worth Rs. 69 lakhs despite several reminders.
He said alternative arrangements had been made from neighbouring Sant Kabir Nagar district to ensure availability of liquid oxygen for the hospital.
Twenty-three children died on Thursday, when, according to the statement, "the pressure of the liquid oxygen supply became low and 52 reserve oxygen cylinders were pressed into service".
"We saw our baby struggling to breathe and we couldn't do anything", Gautam said as tears flowed down his weather-beaten cheek. The death toll for last year was over 600 and this year the hospital has recorded 163 deaths till August 11.
"We are now going back with his body", Gautam sobbed.
Taking a swipe at the Uttar Pradesh health minister, the Congress leader tweeted, "UP Health Minister only seeks votes in Lal Bahadur Shastri ji's name -he doesn't follow Shastri ji's high morals in politics".
India's main opposition Congress party chief Sonia Gandhi and party Vice President Rahul Gandhi have expressed deep shock over the deaths. My thoughts are with the families of the victims. Opposition parties were raising the issue as the government was shying away from its responsibilities, he said. The disease is often spread by mosquitoes, and infections rise during the monsoon season.
An Indian child patient receives medical treament for Japanese Encephalitis at Gaya Medical College in Gaya on September 14, 2015.
Needless to say, complete chaos has prevailed at the hospital as panic-stricken relatives of patients are running post to pillar for help.