Two lingering high pressure systems have trapped warm and humid air above the region, bringing record high temperatures for almost two weeks.
A new record high has been set for Japan, according to the nation's meteorological agency.
The heat, due to a layering of two high pressure systems over much of Japan, is expected to ease slightly this week but temperatures of around 33 deg C are expected.
Less than a month after flooding killed more than 200 people in western Japan, a heat wave has now brought unprecedented scorching temperatures, killing at least 30 people and sending thousands nationwide to hospitals.
Kyodo News agency has tallied more than 40 deaths.
Japan's disaster management agency urged people to stay in air-conditioned spaces, drink water and rest to prevent heat exhaustion.
On the hottest day so far this year, the governor of Japan's capital says that measures to deal with the heat are one of the pillars of the 2020 Tokyo Olympics.
About 1,040 people have fallen ill because of hot weather from May 20 to July 21, an increase of 61% over the same period past year, it said. The central Japanese city of Tajimi, in Gifu prefecture, dealt with temperatures of 104.9 on Monday, after reaching 105.2 degrees last week.
He said: "The actual total human toll may not ever be known as heat-related fatality reports are historically underdone since not all deaths are correctly attributed to heat and some result from accelerating serious health issues and the fatalities show up weeks later".
She said that the city has been working to address heat concerns for both fans and athletes.
"It was the hottest-ever July temperature", Senior Airman Darion DuVerney, a forecaster with the USA 374th Operational Support Squadron, said.
"But our traditional wisdom is not enough to beat the heat like this", she acknowledged, "so we will be using cutting-edge technology".