According to public broadcaster NHK that about 1.3 million residents were ordered or were asked to evacuate, including 80,000 people in Nagoya.
Heavy rains, the approach of Typhoon Roke, caused flooding and damaged roads in dozens of areas of Nagoya and other cities, according to the authorities Aichi prefectural.
In some districts of Nagoya near rivers in flood, emergency workers were helping to evacuate residents by boat.
In Gifu Prefecture, police announced the disappearance of a nine year old child and a man of 84 years, which would apparently fallen into the flood waters.
The Japanese Meteorological Agency said the typhoon was located off the southern coast of Shikoku Island (southwest) on Tuesday night, reports of gusts up to 144km / h.
A typhoon earlier in September left some 90 people dead or missing.