Twelve people died of heatstroke in the week ending July 15 after three perished in the preceding week, according to latest data.
More than 9,900 people were rushed to hospital during the week to mid-July, jumping from 2,700 in the previous week, the Fire and Disaster Management Agency said.
The scorching weather shows no signs of easing.
Kyodo News agency reported that at least 11 people, mostly elderly citizens, died on Saturday alone from suspected heatstroke.
A total of 3,091 ambulances were dispatched in Tokyo on Saturday, a record for a single day, it said.
The weather agency said Sunday's temperatures exceeded 35 degrees C at 233 observation points across the nation by mid-afternoon.
It hit a local record of 39.8 degrees C in the central city of Gujo Sunday afternoon, while in some parts of Tokyo the temperature rose past 37 degrees.
The weather agency issued a warning of extraordinary high temperatures for most regions of Japan's main island.
"Risks of heatstrokes are particularly high," it said, urging citizens to drink enough water and use curtains and air conditioning.
The education ministry has told schools to postpone outdoor activities on hot days. A six-year-old boy died of heatstroke last week after a school outing in sweltering weather.
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