The nation's weather agency issued heat warnings for 38 of Japan's 47 prefectures, telling people to keep hydrated and use their air conditioners.
Sweltering temperatures contributed to the deaths of at least nine people from heatstroke on Saturday and yesterday, Japanese officials and media reports said today.
Another heatwave last month claimed at least a dozen lives.
Japan's record temperature today was registered at 1:42 pm (0442 GMT) in Shimanto, a Pacific coast city on the western island of Shikoku, the Japan Meteorological Agency said.
Temperatures have soared above 40 degrees Celsius for the third straight day across parts of Japan as a Pacific high-pressure system covered most of the country.
The sweltering heat comes as Tokyo's energy costs have soared after Japan shut down its nuclear reactors in the wake of the Fukushima atomic crisis two years ago.
The move forced Tokyo to turn to pricey fossil-fuel alternatives to plug the gap.
Japan stretches some three thousand kilometres from the Okinawa island chain in the south to northernmost Hokkaido.
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