"Average temperatures in Japan are the highest for summer since 1898," the agency said.
From June to August, the agency recorded "considerably higher" average summer temperatures in "northern, eastern, and western Japan".
"The average temperature anomaly in Japan, based on observations at 15 locations, was +1.76 degrees C, far exceeding that of 2010 (+1.08 degrees C), which was the highest since statistics began in 1898 and the highest for summer," it said in a statement.
"Warm air tended to cover northern Japan and warm air flowed in from the south, resulting in considerably higher average summer temperatures in northern, eastern, and western Japan," it added.
The agency said that in many locations such as Itoigawa city "not only maximum temperatures but also minimum temperatures" reached record highs".
The city in Japan's Niigata region recorded a low of 31.4 degrees celsius (88.5 farenheit) on August 10, giving it he highest daily minimum temperature in all of Japan.
Compared to years with particularly high average summer temperatures (2010, 2013, 2018, and 2022), the number of extremely hot days increased significantly from late July onward, reaching the highest total since 2010, it added.
This July was already officially Japan's warmest in 100 years, with at least 53 people dying of heatstroke and almost 50,000 needing emergency medical attention.
Heatstroke is particularly deadly in Japan, which has the second-oldest population in the world after Monaco.
More than 80 percent of heat-related deaths in the past five years have been among senior citizens.
Other parts of the world have also seen record temperatures this summer as climate change makes meteorological conditions more volatile.
July 2023, marked by heatwaves and fires around the world, was the hottest month ever registered on Earth, according to the EU's climate observatory Copernicus.
In France this month late-summer records toppled as a "heat dome" bore down on much of the country, hitting the southern half and Mediterranean coast especially hard.
The Italian city of Milan in late August registered the highest average daily temperature in the past 260 years, regional environmental protection agency (ARPA) said.
Spain has been sweltering under its fourth heatwave of the season, while Greece is struggling for the second time in a month against major wildfires.
Emissions of greenhouse gases are enabling increasingly intense and long-lasting heatwaves, especially in Europe, which the World Meteorological Organization (WMO) says is the fastest-warming continent.
Heatwaves are among the deadliest natural hazards, with hundreds of thousands of people dying from preventable heat-related causes each year.
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