Japan's land ministry and meteorological agency say the Tama River, which flows through Tokyo, reached the evacuation warning level at an observation point in Chofu City at around 1:50 p.m.
The level is used as a benchmark by local governments, which urge residents in surrounding areas to evacuate when it is breached.
Authorities expect the river to continue to swell.
The ministry and the agency are calling on people in 13 areas along the river to be on the alert. The affected areas are the cities of Hachioji, Tachikawa, Ome, Fuchu, Akishima, Hino, Kunitachi, Fussa, Komae, Tama, Hamura and Akiruno.