Typhoon Mindulle made landfall in eastern Japan, roughly 50 miles south of Tokyo, early Monday afternoon local time, causing flooding and significant travel delays.
At least one person is feared dead in the flooding, according to the Japan Times.
Japan's Fire and Disaster Management Agency reported 11 others injured due to the cyclone.
Tokyo's Narita Airport was closed Monday afternoon when winds of 126 km/h (78 mph) lashed the control tower, forcing employees to evacuate.
This was the first time that the tower has ever been closed due to a typhoon, according to the Associated Press.
Torrential rain and strong winds resulted in the cancellation of more than 400 flights in and out of Tokyo's airports on Monday.
Heavy rain totaled nearly 300 mm (12 inches) in Oshima while the Greater Tokyo area received 75-150 mm (3-6 inches) as of early Monday evening.
The flooding caused further travel delays as many roads were left underwater.
Heavy rain triggered a mudslide resulting in the evacuation of a commuter train in western Tokyo, according to the Associated Press.
Rivers will remain swollen into Tuesday as the threat for flooding and mudslides continue.
The heaviest rain from Mindulle will shift into Hokkaido into Tuesday where flooding is ongoing following the landfall of Tropical Storm Kompasu on Sunday.
An additional 75-150 mm (3-6 inches) of rain is expected across Hokkaido through Tuesday.