Hundreds of mainly children die across India each year from the mosquito-borne virus, but West Bengal is not normally one of the worst-hit states.
Only five people died last year in West Bengal from Japanese encephalitis, one form of the virus which normally hits during the monsoon season when mosquitos breed.
West Bengal health services director Biswaranjan Satpathy said late on Monday there had been a sudden spike in cases and deaths between July 7 and 20.
Satpathy chaired a meeting of state medical officers on Monday to assess the situation that he said had reached "alarming proportions".
He said there was no specific reason for the jump, and instead cited "seasonal variance".
"It wasn't like this in June, it suddenly shot up," Satpathy also told reporters on Tuesday, while visiting a hospital in Siliguri, some 460 kilometres (285 miles) north of state capital Kolkata.
"We are dedicated to this. The cases are happening and that's why people are here. We are trying to help everyone," he said.
India's most populous states of Uttar Pradesh and Bihar further north are ravaged by encephalitis every year as mainly malnourished children succumb to the disease.
Encephalitis causes brain inflammation and can result in brain damage. Symptoms include headaches, seizures and fever.
Health experts say 70 million children nationwide are at risk.
National health minister Harsh Vardhan last month ordered "extraordinary steps" to end encephalitis, including an immunisation drive and dedicated hospital beds for encephalitis patients in affected districts.
Although there is a vaccine for Japanese encephalitis, mainly children die from other forms of the disease, including acute encephalitis syndrome, the exact causes of which are not known.