The incident took place, authorities say, at around 8 p.m. (7 a.m. ET) on a train on the Keio railway line, NHK reported.
The train was operating near Kokuryo Station, in the city of Chofu, west of Tokyo.
The suspect was also reported to have scattered cigarette lighter fluid in the train car, which he then set ablaze.
At least 17 people were injured, NHK reported citing police. One of the victims, a man in his 60s, is seriously injured and unconscious, the broadcaster added.
Police said a man in his 20s, carrying a knife, has been taken into custody, according to NHK.
The train operator said in a tweet that the train’s operation has been stopped due to the incident.
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