Typhoon Mindulle made landfall at about 12:30 pm (0330 GMT) in Tateyama city, 80 kilometres (50 miles) southeast of Tokyo, the Japan Meteorological Agency said.
As of 2:00 pm, the storm was packing gusts up to 180 kilometres per hour. It was sited near the city of Chiba, 30 kilometres east of Tokyo, and heading north at a speed of 20 kilometres per hour, the agency said.
There were no immediate reports of casualties or significant damage.
"In Tokyo... please exercise caution for landslides, flooding in low-lying areas, surging rivers, violent wind and high waves," the weather agency said.
Downpours across the greater Tokyo region caused rivers to swell, with gushing waterways close to overflowing but staying within their banks.
Narita international airport east of Tokyo closed its runways in the afternoon for about an hour as officers evacuated the control tower due to strong winds, according to the airport operator.
The storm has caused airlines across the country to cancel a total of 425 flights, mostly to and from Tokyo's Haneda airport, national broadcaster NHK said.
Japan Airlines said it cancelled 185 domestic flights, affecting 33,692 customers, while All Nippon Airways cancelled 112 domestic flights, affecting 26,500 passengers.
Most major commuter train services in Tokyo and its surrounding region operated normally, including bullet trains.
Some lines, however, suffered temporary delays and stoppages.
Separately, Typhoon Kompasu, which hit Japan's northern main island of Hokkaido Sunday, was downgraded to a temperate depression by early Monday as it moved away into the Sea of Okhotsk.
Heavy rain since Saturday caused high waves and rivers to flood on the island, where rescue workers found a male body Monday morning.
Police did not immediately link the death to the storm, but local media said it might be the owner of a vehicle stranded by heavy rain.
The local Hokkaido government has said the storm has caused only three minor injuries so far.
