The typhoon, which is accompanied by high winds, has also led to the early closure in the capital of one of the world's biggest video game trade fairs and knocked out power for thousands, AFP reported.
The Japan Meteorological Agency (JMA) warned on Sunday that rain and winds were expected to intensify even before the typhoon's arrival.
"The total rainfall through Tuesday could exceed the average monthly rainfall for September, resulting in record-breaking heavy rain," the agency said.
The typhoon's wind speeds were at 144km per hour as the storm was approximately 110 kilometers from Hachijojima, one of Tokyo's farthest islands.
On Monday, more than 4,000 households in Chiba, next to Tokyo, were without power, while the JMA and local authorities warned residents of heavy rain and possible landslides.
Japan Airlines cancelled 120 domestic and 15 international flights, while All Nippon Airways cancelled 140 domestic flights.
Railway operators in Tokyo and neighboring regions suspended services on some lines.
Tokyo Game Show, one of the world's biggest video game trade fairs, which kicked off on Thursday, was called off on Monday, its final day.
A major outdoor music festival and a baseball match, both scheduled to be held in Chiba, were also cancelled.