A tornado is seen in Tsukuba, north of Tokyo, in this picture taken by a resident yesterday. REUTERS/Kyodo
The boy was pronounced dead in hospital after a twister ripped through Tsukuba city, 60km northeast of Tokyo yesterday afternoon.
More than 30 people were injured and at least 200 houses were damaged in the city, public broadcaster NHK reported.
Another tornado hit Moka city and neighbouring areas, 80km north of Tokyo, injuring nine people and damaging more than 360 houses, NHK reported.
Television footage showed dozens of houses without roofs and many more with shattered windows.
According to the Tokyo Electric Power Co, more than 20,000 homes lost power after the twisters hit the region.
The Meteorological Agency issued tornado warnings in central, eastern and north-eastern Japan, including Tokyo.
