The average temperature nationwide between June and August was 1.64 degrees Celsius above average for the period, forecasters said.
The previous record margin was 1.36 degrees C set in 1994.
The agency did not say what the average temperature was, but Tokyo’s summertime temperatures averaged 27.1 degrees C (80.78 Fahrenheit).
In August, the mercury often soared above 35 degrees C in many areas of the country, the agency said.
“It can be said that weather was abnormal in this summer,” an agency official, Shuhei Maeda, told a news conference. “The temperature is forecast to exceed 35 degrees centigrade in many places for a week to come.”
Scorching summer weather led to at least 132 deaths and saw more than 30,000 people taken to hospital with heatstroke, the government said in mid-August.