NHK said passengers reported an explosion in a bathroom in another part of the same car, near where the other passenger who died, a woman, was found lying immobile.
The train, which was bound from Tokyo to the western city of Osaka, made an emergency stop on a stretch of track southwest of the city of Yokohama, NHK said. Television images showed emergency crews and railway workers surrounding the train.
The fire was extinguished soon after it was discovered, NHK said, but about 20 other passengers were being treated for smoke inhalation.
The female passenger suffered heart failure, according to the network.
No information was immediately available about the identities of the people killed, or about possible motives behind the incident.
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