Tokyo was among the most affected with 1,095 hospitalizations, followed by 989 in Aichi Prefecture, 805 in Saitama and 801 in Osaka.
Temperatures reached 102 degrees Fahrenheit in some prefectures at the peak of the heatwave over the weekend.
Meteorologists expect temperatures below 99 degrees in major Japanese cities on Tuesday.
To battle the longstanding heat, they urge citizens to use air conditioning, avoid going outside and drink enough water.
Almost 40 Japanese nationals died from heatstroke since June, while some 25,000 have been admitted to hospitals, according to the agency which also oversees emergency services.
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