Typhoon Mindulle made landfall at about 12:30pm local time (04:30 GMT) in Tateyama city, some 80km (50 miles) southeast of the capital.
The storm packed gusts of up to 180 km/h (112 mph), and was headed north at a speed of 20 km/h, the Japan Meteorological Agency said.
Officials have warned of landslides and flooding.
"In Tokyo... please exercise caution for landslides, flooding in low-lying areas, surging rivers, violent wind and high waves," said the weather agency.
There were no official reports of casualties, however local media reports said at least two are feared dead.
The storm caused airlines across the country to cancel about 400 domestic flights, local media said, with the majority going to and from Tokyo's Haneda airport.
In the afternoon, Narita International airport briefly closed its runways.
Japan Airlines said it had cancelled 185 domestic flights, according to Nikkei news agency. All Nippon Airways also said 112 domestic flights had been cancelled.
Most major commuter train services in the Tokyo area were operating normally, according to East Japan Railway.
A strong typhoon packing heavy rain and wind has struck near Tokyo, grounding hundreds of domestic flights.