It was not immediately clear what was behind the passengers' complaints and they were not seriously ill, local media said.
Police confirmed there was an incident at Takadanobaba station without giving further details.
TV footage showed police, emergency crews and ambulances on the scene.
The incident, which began around 5:45 pm (local time) fanned fears in a city still horrified by deadly sarin gas attacks two decades ago.
Last year, the final suspect in the 1995 nerve gas attack on the Japanese capital's metro was jailed for life for his part in a crime that shocked the world.