Health and family welfare minister Pradip Kumar Amat told reporters here that 93 children had died in Malkangiri district, of which 32 were suferring from JE.
The health minister, however, attempted to downplay the situation and claimed that 61 kids died of some other diseases.
He said that currently 17 children were undergoing treatment at the district headquarters hospital in Malkangiri.
Out of them, six were in the Intensive Care Unit while 11 were undergoing treatment in the Encephalitis ward, he added.
The Health Minister said that 180 villages in seven blocks of the district were affected in the vector-borne disease.
Claiming that the state government has distributed 15,000 Insecticide Treated Mosquito Nets (ITMN) to check the spread of vector-borne disease, Amat alleged that Odisha was yet to receive the ITMN provided by the Centre.
The minister said the vaccination programme against JE would begin in Malkangiri district by December.
Rejecting the minister's statement, state BJP president Basant Panda claimed that the JE death toll in Malkangiri along was above 100.