Amid very active thunderstorms, the twister struck Ibaraki and Tochigi prefectures, some 35 miles northeast of Tokyo around 1 p.m., the Kyodo news agency reported.
Police said as many as 250 houses lost roofs and windows to the funnel cloud, which has not yet been officially recognized as a tornado by meteorological officials.
At least 40 people were injured, two of them seriously. One of them, a 14-year-old boy, died of his injuries in a hospital, the report said.
The thunderstorms also caused widespread reports of lightning damage and disruptions and delays in bullet train service along the east coast, Kyodo said.