More than 3,000 homes were without electricity Monday, a day after apparent tornadoes tore through eastern Japan, killing one person and injuring at least 46 more.

Nearly 900 houses were damaged as gusting winds whipped through the prefectures of Ibaraki and Tochigi, near Tokyo, splintering wooden homes and tearing down trees and power cables.

The only known fatality from the storms, which hit on Sunday afternoon, was a 14-year-old boy who was crushed to death when his house collapsed, officials said.

The government's Fire and Disaster Management Agency said 36 people were injured in Ibaraki, on the northern edge of a plain stretching from the capital, and 440 homes were damaged, some of them badly.

In the neighbouring prefecture of Tochigi, about 450 houses were hit and nine people were injured. One person was injured in another prefecture on the plain, the agency said.

A spokesman for Tokyo Electric Power, the utility that supplies the area, said of the more than 19,000 homes that lost power when the storms hit, more than 3,000 were still without electricity at midday on Monday.

Several clips of amateur video footage aired by local broadcasters showed twisting columns of wind wreaking havoc as they tore through residential areas.

Scientists say tornadoes, which are commonly associated with North America, are difficult to predict.

Japan's meteorological agency issued 589 warnings in 2011, but only eight actual tornadoes occurred.

"We have to use past data and projected data to make our predictions in given places," said an agency spokesman. "You cannot observe it using radar.

"Because it is something that we cannot directly predict using observed data, our forecasts are less accurate than regular weather forecasts or those for typhoons."