An agency spokesman warned that “unprecedented levels of heat” were being seen in some areas.
More than 22,000 people have been taken to hospital with heat stroke, nearly half of them elderly, officials say.
On Monday, the city of Kumagaya reported a temperature of 41.1C (106F), the highest ever recorded in Japan.
The heatwave shows no sign of abating, forecasters say.
In central Tokyo, temperatures over 40C were also registered for the first time.