Footage on public broadcaster NHK showed a number of homes destroyed, upturned cars, schools with shattered windows and a warehouse that had been lifted from its foundations and hurled into other buildings in Koshigaya, north of Tokyo.
An AFP journalist in the city saw roof tiles scattered all over the streets, with locals outside inspecting their battered homes and emergency vehicles at the scene.
Residents were being prevented from re-entering their houses for fear of collapse.
Some electricity poles had been snapped and a number of them had hit houses as they fell, worsening the damage.
The Koshigaya city hall said 29 people were injured, three of them seriously, in the city alone.
Jiji Press agency said most of the injured were members of a volleyball team at a local middle school.
“We are preparing evacuation shelters, while also readying emergency supplies,” said an official of the fire department in Koshigaya.
The electricity supply was cut for some 33,000 households in the region, mainly in Saitama prefecture, probably after lightning strikes, according to utility Tokyo Electric Power which provides power in the area.
“Weather conditions in the region today have been very unstable,” said a meteorologist at Japan’s weather agency.
“In flatter parts of the region particularly, warm, wet air can come inland and spark tornados. This is especially the case when there is a typhoon developing in the south,” he said.