Television footage showed badly damaged houses in Yaita, north of Tokyo, some with their roofs peeled off.
Local rescuers had not received any reports of injuries about an hour after the winds smashed through the area, a local official said.
"The roof of a school gymnasium was torn off, and the power supply is cut off," he said. "Traffic lights are not working either."
Pictures posted on Twitter and other social networks showed a dark funnel of cloud stretching down to the ground, whipping up debris.
A total of 63 people were injured and about 110 houses were damaged or destroyed in Koshigaya and surrounding areas.