More than 22,000 people have been admitted to hospital with heat stroke, nearly half of them elderly, emergency officials say.
Japan's weather agency has declared a heatwave sweeping the country a natural disaster, with little let up in sight until early August.
More than 65 heat-related deaths have been recorded in the past week.
“We are observing unprecedented levels of heat in some areas," a Japan Meteorological Agency spokesman Motoaki Takekawa said, adding that the heatwave was "a threat to life and we recognise it as a natural disaster".
More than 22,000 people have been admitted to hospital with heat stroke, nearly half of them elderly, emergency officials say.
On Monday, the city of Kumagaya reported a temperature of 41.1C (106F), the highest ever recorded in Japan.
In central Tokyo, temperatures over 40C were also registered for the first time.
The BBC says people in some cities have taken part in an event known as uchimizu, or "water ceremony" - pouring or sprinkling cold water on to the hot pavements in an attempt to cool them.
The high temperatures follow record rainfall that caused floods and landslides in western and central Japan, killing more than 220 people.
The extreme weather has reignited concerns about the Tokyo Olympics in 2020, which will be held in July and August.