As of Monday, the number of people who have been taken to hospitals by Tokyo's ambulances due to heatstroke this year stood at 3,544, already surpassing the 3,454 for the whole of last year, according to the department's preliminary report.
The two-week heatwave also claimed the life of a six-year-old boy who died after participating in a school lesson outside.
Japan on Monday recorded its highest ever temperature of 41.1 degrees Celsius in Kumagaya in Saitama Prefecture, around 80 kilometres from capital Tokyo.
Where was Japan's hottest ever temperature recorded?
Tokyo's postwar high temperature in August averages 31.5 C (88.7 F).
The soaring temperatures have also impeded the continuing relief efforts after Japan earlier in July witnessed its most deadly flooding in decades, with 222 casualties confirmed so far.
The temperature rose to a record 41.1 Celsius (106 Fahrenheit) in a city northwest of Tokyo on Monday, as a heat wave in Japan that has killed at least 23 people and sent thousands to hospital showed no sign of significant easing.
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Tourists in Tokyo's historic Asakusa district struggled with the heat.
High-risk groups included elderly people and individuals with pre-existing conditions such as asthma and heart failure, Dr Myers warned.
How long is the heatwave expected to last?
She said that the city has been working to address heat concerns for both fans and athletes.
The record-setting heat in Kumagaya, north of the capital, was recorded at a Japan Meteorological Agency observation point at 2:16 p.m.
"And even at lower temperatures, the heat can be unsafe for small children and elderly people, and depending on the environment and activities you are doing", the official warned.
"People should be all the more careful as many people must be exhausted after days of cruelly hot weather", she added.