The plurality of people — 45.4 percent — were affected by the heat while at home, while 17 percent called an ambulance while at work, the agency said.
Of nearly 12,800 such calls, almost 4,000 were made by the elderly, while 387 people are still in a critical state.
The temperature in Tokyo and other parts of Japan is keeping up to 38 degrees Celsius (100.4 degrees Fahrenheit).
This time of year always brings extreme temperatures to Japan, and authorities are used to keeping a record of related casualties. Last year, the heating season left 126 people killed and more than 70,000 others hospitalized with heat-related health complications.