A woman from Tokyo died after falling into a river and being washed 10 kilometers (6 miles) downriver to Yokohama, police said. Two sixth-grade boys and another person were missing on Japan's main island, Honshu, the Fire and Disaster Management Agency said.
More than 350 homes were damaged or destroyed, including 283 on Izu Oshima, it said.
The typhoon, which stayed offshore in the Pacific, had sustained winds of 126 kilometers per hour (78 miles per hour), with gusts up to 180 kph (110 mph), before it was downgraded to a tropical storm Wednesday evening. The storm was moving northeast, off the northern Japanese island of Hokkaido.
More than 80 centimeters (30 inches) of rain fell on Izu Oshima during a 24-hour period ending Wednesday morning, the most since record-keeping began in 1991.
The rainfall was particularly heavy before dawn, the kind in which "you can't see anything or hear anything," Japan Meteorological Agency official Yoshiaki Yano said.