The mercury reading for Tokyo's financial district at 12:58 pmwas the highest in the capital since the agency began recording data in 1923, surpassing the previous record of 39.1 Celsius reached on August 3, 1994, an agency official said.
At least 12 people, six of them in their 60s or older, were taken to hospital for treatment of heatstroke in the capital, a spokesman for the Tokyo Metropolitan Fire Department said. None of them was in serious condition.
"We'd better not stay outside. But it won't be easy," said Taisuke Nakamura, a 57-year-old employee, sweating profusely on the downtown streets of the Ginza shopping district.
Postal worker Katsuaki Kujirai, 53, said: "There is nothing I can do but take water."
Another agency official said the record temperature was brought about by warm, dry winds from the mountains surrounding Tokyo and its vicinity.
The hottest place in the country was Ushiku, a rural city some 30 kilometers (20 miles) northeast of Tokyo, which hit 40.2 C.
The reading was just short of Japan's all-time high of 40.8 C registered in Yamagata, 300 kilometers (190 miles) north of Tokyo, on July 25, 1933.
A short rainy season in many parts of the country and the hot and humid weather have claimed several lives and caused more than 300 people to collapse and require hospital treatment so far this month.
Floods and landslides triggered by torrential rains over coastal areas in northern Japan have claimed at least 18 lives.
The Meteorological Agency has warned the public to take measures against heatstroke as a 40-day summer break started Tuesday at most primary to high schools across the country.
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