Tropical storm Malou has dumped heavy rains in much of Tokyo and the surround areas on, some places registering record rainfalls of 100 mm per hour.
Heavy rains swelled rivers, some which burst their banks and flooded residential areas and destroyed bridges.
In other areas, the rainfall overwhelmed the sewage system which then also flooded streets.
So far there has been no reports of any injuries but at least two men, believed to be living in shacks near a major river, were trapped as the rising waters surrounded them and had to be rescued.
The storm earlier in the day was considered typhoon-strength by Japanese standards and had been the ninth typhoon of the season in the north eastern Pacific but the first to hit land northwest of Tokyo.
Typhoons usually swerve across the nation from the southeast but meteorologists blame this summer's unusually strong high pressure patterns for the unexpected storm path.
It also brought the capital its first rains in a month, helping alleviate what had been the longest and hottest heatwave in its history.
3 News / Reuters