"As a record heatwave continues to blanket the country, urgent measures are required to protect the lives of schoolchildren", top government spokesman Yoshihide Suga told reporters Tuesday.
More than 22.6 thousand people were hospitalized with heatstroke symptoms.
Less than half of Japan's public schools have air conditioning, and the figure is only slightly higher at public kindergartens. Government agencies have warned that the country's 35 million senior citizens are particularly vulnerable to the heat; at least 80 per cent of the casualties have been among those age 65 and above, a researcher told Reuters.
Officials are working to combat the heat, with one effort supplying funds to all schools to ensure air conditioners are equipped by next summer.
Japan logged its highest ever temperature on Monday, as the temperature in Kumagaya, a city in Saitama prefecture near Tokyo, hit a record high of 41.1 degrees Celsius.
Temperatures over 40C were registered for the first time in Tokyo's metro area, where the government is promoting uchimizu, a tradition where water is sprinkled on to the ground, as part of a summer heat awareness campaign.
It was marginally cooler yesterday, but temperatures remained well above normal in most of the country. "We recognize it as a natural disaster".
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"We are observing unprecedented levels of heat in some areas", agency spokesman Motoaki Takekawa said, adding that the heatwave was "a threat to life and we recognise it as a natural disaster".
Officials have urged people to use air conditioning, drink sufficient water and rest often.
The Japan Meteorological Agency is predicting that high temperatures will continue for the next two weeks, and called for caution.
The heatwave closely followed torrential rain that caused severe flooding and landslides in the west of Japan.
Japan has for days been in the grip of a deadly heatwave, although the numbers reported killed vary widely from 15 to as high as 40.
The broiling heat has also fueled worries for the safety of athletes and spectators at the Tokyo Summer Olympics in 2020.
"The weather recently in Tokyo and across Japan is like being in a sauna", Tokyo Gov. Yuriko Koike said at a news conference.