Of the 2,978 children admitted this year at different hospitals in Gorakhpur and Basti division, 623 died of the disease, as per the data from the office of Additional Health Director.
"The government was concentrating on eradicating mosquito-borne encephalitis, whereas 98 per cent patients suffer from water-borne encephalitis to which no attention was paid," R N Singh, a senior child specialist doctor and a crusader against the disease, said.
Water-borne encephalitis spreads due to contaminated water and malnutrition, but the government has not taken steps to check the root causes of the disease, he said.
The disease claimed 1,135 lives in 2005, 434 in 2006, 547 in 2007, 515 in 2008, 568 in 2009, 543 in 2010, 655 in 2011 and 608 in 2012, as per the data.
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Ruing that there was no major decline in number of deaths due to encephalitis, Singh said in 2011, a national programme proposed by a Group of Ministers is yet to be implemented.
The government was concentrating on treatment and not prevention, he said, and alleged that the state and Centre were "merely indulging into politics over the issue".