Typhoon Faxai has made landfall near the Japanese capital bringing heavy rain and winds of up 210km/h (130mph).
Hundreds of thousands in the greater Tokyo area have been advised to evacuate as forecasters warned the rain and wind could break records.
The storm has affected transport with about 100 bullet trains and 100 flights cancelled in the region.
It comes after North Korea was hit by a separate typhoon on Sunday leaving five people dead.
According to Tokyo Electric Power company, about 290,000 households lost power as Faxai made landfall.
Authorities issued non-compulsory evacuation warnings to more than 390,000 people in Kanagawa, Shizuoka and Tokyo prefectures.
JR East, the main suburban railway operator in greater Tokyo, has cancelled trains in the area until 08:00 on Monday (23:00 GMT Sunday) to allow early morning track inspections for possible damage.
Faxai is now travelling north at 25km/h and is expected to hit northeastern Japan.
Authorities in the country have warned of possible landslides and swollen rivers.
The storm comes as the country is preparing to host the Rugby World Cup.
England manager Eddie Jones says his side have got to “ride with it”, while contingency plans are in place before the tournament starts on 20 September.
The Australian team’s arrival was delayed by the storm.
On Saturday, Typhoon Lingling passed over North Korea, flooding 460 sq km (178 sq miles) of farmland, the official KCNA agency said.
There are concerns that the storm could worsen already severe food shortages in the country.
Earlier this year, the UN warned that up to 10 million North Koreans were “in urgent need of food assistance.”