The mercury hit 39.1 Celsius (102.4 Fahrenheit) in Yamanashi in the centre of the country today, while dozens of other spots recorded temperatures of 35 Celsius or more.
A total of 2,594 people were hospitalised in the first week of July due to the effects of heat, with three of them dying, the fire and disaster management agency said in a report.
More than 42 percent of them were aged 65 or older, the agency said.
News reports feature frequent reminders to drink plenty of fluids and avoid prolonged periods outdoors, in what has become a regular feature of the sticky summer months.
The heat wave struck nationwide this week with high-pressure systems sitting over the Japanese archipelago, bringing an earlier than usual end to the rainy season.