Eight towns and one city on the island recorded their highest temperature since 1977 when official data became available, the Japan Meteorological Agency (JMA) said.
Bihoro town was the hottest in Hokkaido with the mercury hitting an energy-sapping 38.2C on Wednesday afternoon.
"We are calling for residents be vigilant about heat strokes through our official website and social media messaging app," Ryo Nakachi, a government official in the neighbouring city of Kitami, told AFP.
Kitami opened its "cooling shelter" to residents, many of whom do not have an air conditioner in their home, he said.
A JMA meteorologist in Hokkaido said the clear sky, flows of warm air from China and warm, dry down-slope winds caused Wednesday's high temperatures on the island.
Japan's environment ministry issued a heat stroke alert on Wednesday to a swath of the archipelago including half of Hokkaido.
The highest temperature ever recorded in Hokkaido is 39.5C in May 2019 in Saroma, JMA meteorologist Akiko Miura said.
The scorching temperatures comes after Japan experienced its hottest June on record, as climate change prompts sweltering heat waves across the globe.
With strong high-pressure systems in June staying in the region, the average monthly temperature was 2.34C higher than the standard value, the JMA said earlier this month.
Japan's summer last year was the joint hottest on record, equalling the level seen in 2023, followed by the warmest autumn since records began 126 years ago.
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