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NHK public television said at least 10 passengers were injured, including one seriously.
The attacker, only identified as a man in his 20s, was arrested on the spot and is being investigated, NHK said.
Tokyo police officials said the attack happened inside the Keio train near the Kokuryo station.
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Television footage showed a number of firefighters, police officials and paramedics rescuing the passengers, many of whom escaped through train windows.
The attack was the second involving a knife on a Tokyo train in two months.
In August, the day before the Tokyo Olympics closing ceremony, a 36-year-old man stabbed 10 passengers on a commuter train in Tokyo in a random burst of violence.
The suspect later told police that he wanted to attack women who looked happy.