The temperature in Kumagaya, a city in Saitama prefecture near Tokyo, hit a record high of 41.1 degrees Celsius around 2:00 p.m. local time (0500 GMT) on Monday, said the Japan Meteorological Agency (JMA).
It was also the highest temperature ever logged across Japan, said the agency, warning against heat-related illnesses, such as heatstroke and dehydration.
Temperature in Ome city of Tokyo Metropolis reached 40.8 degrees Celsius around 2:00 p.m. local time (0500 GMT), the first time for an observation point in Tokyo Metropolis to surpass 40 degrees Celsius.
A protracted heatwave has been scorching wide swathes of Japan in recent weeks, causing the deaths of more than 40 people and tens of thousands were hospitalized, according to local media.
According to the Kyodo News, at least 11 people died Saturday from suspected heatstroke across Japan with a record number of ambulances dispatched in Tokyo to send people to hospitals.