Two people were reported to be in cardiac arrest after smoke was detected on the train, which was bound for the western city of Osaka from Tokyo.
Footage on TBS television showed a train carriage filled with smoke and passengers evacuating with handkerchiefs pressed to their faces.
One clutched a baby to their chest.
No further details were immediately available.
Japan's superfast Shinkansen trains have until now been known for their speed and their safety.
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