At least nine people were killed and over 100 injured on Sunday after a heavy typhoon Hagibis hit Tokyo metropolitan area, with many rivers overflowing into residential areas.
Store shelves were bare after people stocked up on water and food ahead of Typhoon Hagibis.
The Japan Meteorological Agency warned of dangerously heavy rainfall in Tokyo and surrounding prefectures, including Gunma, Saitama and Kanagawa.
Authorities said that about 260 people were stranded in a nursing home due to floods in Saitama prefecture, north of Tokyo, where they were using boats to rescue the stranded seniors and staff members.
Some 14,000 households in eight prefectures were without water supplies in the wake of Hagibis.
In the early hours of Sunday, 4,540 households in Marumori in Miyagi prefecture did not have tap water service.
Earlier on Friday, hundreds of flights and trains were cancelled in Japan ahead of the arrival of super typhoon Hagibis, considered one of the most powerful storms in the Pacific this season.
The typhoon will approach the southwestern half of the country and will advance towards the centre and northeast of the country over the weekend, according to the Japan Meteorological Agency (JMA).
Torrential rain and tornado-like winds were lashing large parts of Japan, as the country endures what could be its worst storm for 60 years, the BBC reported.
Hagibis made landfall shortly before 7 pm on Saturday, in the Izu Peninsula, south-west of Tokyo.