Heavy rains and strong winds battered Tokyo on Monday as Typhoon Man-yi made landfall in the southern Aichi prefecture some 200 miles (320 kilometres) away from the capital.
The arrival of Man-yi halted transportation and prompted evacuations across three prefectures in the midwestern part of the country.
The eye of the storm is expected to head in a northeastern direction at 45 kph (28 mph), passing through the metropolitan Tokyo area and heading towards the northern Tohoku area in the afternoon.
Japan's Meteorological Agency has issued the highest level emergency weather warnings across three prefectures - in Kyoto, Fukui and Shiga - where heavy rainfall was recorded early on Monday.
The emergency weather warning is part of a new system which was launched on 30 August and is issued by the agency when there is significant likelihood of catastrophes due to severe weather that far exceeds a warning criteria.
The agency has issued evacuation orders for thousands of households in the three prefectures.
Weather warnings for heavy rain, flood and storm have also been issued across much of the Honshu mainland, including the Tokyo area.
Transportation has been affected, with broadcaster NHK saying more than 500 flights nationwide have been cancelled. The Tokaido Shinkansen bullet train has also been suspended.