The rise in temperatures had prompted the national weather agency to issue heat wave advisories for 41 of the country's 47 prefectures.
According to the tally, the preliminary figure of people being rushed to hospitals was 1,389, of whom five died and 20 were in serious condition.
Of 927 observation points of the Japan Meteorological Agency nationwide, 702 -- more than 70% -- logged highs of at least 30 degrees Celsius, while about a quarter of all locations topped 35C.
The city of Higashiomi in western Japan's Shiga Prefecture hit a record-breaking 38.8C. At 13 other locations, the mercury reached record highs, including Obama in Fukui Prefecture on the East Sea/Sea of Japan coast, at 38.7C.
According to the agency, a high-pressure system in the Pacific Ocean sent a blanket of warm air over a wide swath of the archipelago from the Tohoku region in the northeast to the southern island prefecture of Okinawa.
A cold front heading south is forecast to bring the possibility of cooling rain over the country on Sunday, but the stifling heat will likely return on Monday and is expected to continue, the agency said.