The fatalities were recorded in 28 of the 47 prefectures in a seven-day period through Sunday as most of the Japanese archipelago experienced unusually high temperatures, according to the Fire and Disaster Management Agency.
The heat is expected to ease slightly this week as a high pressure zone responsible for it moves west and east, allowing moist air to bring rain to some scorched areas, the Japan Meteorological Agency said.
Recall, meteorologists recorded the highest temperature ever recorded in Japan - to 41.1° C. the Record was recorded near the city of Kumagaya in Saitama Prefecture North of Tokyo.
More than 40 people have died in Japan and about 10 in South Korea of heat-related causes this summer. Temperatures topping 40 degrees Celcius were reported there for the first time on Monday.
The heatwave "is fatal, and we recognise it as a natural disaster", he told reporters.
"People in areas where temperatures are as high as 35 degrees or higher should be extremely careful" to avoid heatstroke, a meteorological agency official told news agency AFP.
Tourists in Tokyo's historic Asakusa district struggled with the heat.
"As a record heatwave continues to blanket the country, urgent measures are required to protect the lives of schoolchildren", said Yoshihide Suga, Japan's chief cabinet secretary. Right now, fewer than 50 percent of the country's public schools have air conditioning.
But Greece has seen the worst effects of the heat, with devastating wildfires around the capital killing at least 50 people and injuring hundreds more.
Layla Tan, 28, an global business adviser, said she felt heat exhaustion on Sunday.
The public is being advised to drink plenty of water, to use air conditioning and to rest often. Earlier this month, a representative of the International Olympic Committee said steps were being taken to minimize the impact of Japan's summer heat on the Games, the Wall Street Journal reported.
The current heatwave being the hottest on record has raised some concerns about the 2020 Summer Olympics in Tokyo.