The mounting death toll has highlighted the deteriorating condition of India's health department, five years after a similar encephalitis outbreak led to the deaths of over 350 children in Bihar state, one of India's poorest, in 2014.
Hospitals and intensive care units across Muzaffarpur are experiencing an acute shortage of doctors and vital medical personnel,
On Monday India's Supreme Court accused the Bihar state and federal governments of negligence.
Dr Arun Shah, a paediatrician in Muzaffarpur, believes that chronic malnourishment is the reason behind the rising number of encephalitis deaths.
The Muzaffarpur district is known as the 'lychee bowl of India', with studies and members of the public pointing to the exotic fruit as a potential cause for the brain fever related deaths of children, India Today says.
Lychee - known as litchi in India - contains natural toxins including hypoglycin A which leads to a reduction in blood sugar levels during sleep.
But lychee fruit is also a rich source of vitamin B, calcium, iron, phosphorus and potassium, and any connection between encephalitis and lychee consumption was discounted by the Director of India's National Research Centre on Litchi, Dr Vishal Nath.
Dr Nath said it is "very unfortunate that people have been misled about the fruit".
Kaushal Kishor, Bihar's additional heath secretary, agreed, telling Al Jazeera: "It's all guesswork. There is no conclusive evidence that lychees cause this disease."
Dr Nath did note that while lychee are perfectly safe to eat, it is advisable not to eat the acidic fruit on an empty stomach.
India's Prime Minister Narendra Modi has made no public statement on the crisis.
Indian Health Minister Harsh Vardhan said the PM is "monitoring the situation", according to Reuters.
