Officials with Japan's land ministry and meteorological agency say the Tama River, which flows through Tokyo and neighboring Kanagawa prefecture, reached the flood risk level at an observation point at around 3:40 p.m. on Saturday.
Authorities expect the river will continue to swell.
The level serves as a benchmark which local governments use to draw up evacuation advisories for residents in surrounding areas.
The ministry and the agency have issued flood risk information to nine areas along the river and are calling on people to be on alert for flooding.
The affected areas are Setagaya Ward, the cities of Fuchu, Chofu, Hino, Kunitachi, Komae, Tama, and Inagi in Tokyo, and Kawasaki City in Kanagawa prefecture.