More than 1,000 other people were forced from their homes by the flooding brought by Typhoon Lionrock.
The body of a man was also found near a river in Iwaizumi and a dead woman was found in Kuji city, police said.
Television pictures showed flooded rivers with cars and homes partly submerged, while rescuers picked up stranded people by helicopter.
Several people were also missing on the northern island of Hokkaido, police said.
Iwate, the worst-hit prefecture, was devastated by a massive earthquake and tsunami in March 2011.