Around 10 million children were vaccinated against the virus, said Anant Kumar Singh, the top medical official in the northern state of Uttar Pradesh.
"In total 42 districts are prone to the virus but due to a shortage of vaccine, only 18 have been fully covered," Singh said.
The deaths were also reported from areas where children were immunised.
The virus, which can result in brain damage, claimed more than 400 lives last year and over 1,400 in 2005 in the state -- India's most populous with 180 million people and one of the poorest.
Encephalitis, or brain fever, is endemic to the eastern part of the state, with the virus often passed on to human beings from pigs.
In the past 26 years, around 5,000 lives have died from a strain known as Japanese encephalitis, which causes blinding headaches, seizures, nausea and a high fever that usually precedes death.