The typhoon made landfall in Toyohashi, Aichi prefecture, shortly before 8:00 am local time (0430 IST), packing gusts of up to 162 kilometres (100 miles) per hour, the Japan Meteorological Agency said.
Public broadcaster NHK said a woman in her 70s was missing following a landslide in Shiga prefecture, while at least six people were injured in other areas due to strong wind.
The typhoon, moving north-northeast at a speed of 45 kilometres per hour, is expected to head towards the capital and its surrounding region later in the day, the agency said.
About 350 domestic flights scheduled for today, a public holiday, were cancelled, mainly those departing Tokyo, and train services were also reduced, NHK reported.
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The typhoon was expected to cross the northeast, including the Fukushima area, today afternoon possibly bringing heavy rain to areas near the crippled nuclear power plant, according to its predicted track.
Crews have struggled to contain the nuclear plant after the March 11, 2011 earthquake and tsunami that triggered the atomic disaster and led to the contamination of groundwater with radioactive materials as it flows to the Pacific Ocean.
The typhoon had already brought heavy rain and strong winds to the south and east before even hitting Japan.