World Athletics chief executive Jon Ridgeon said the organisation’s health and science team had assured him the schedule change would make a “significant difference to the athletes”.
Ridgeon added it was not possible to move the start time any earlier than 07:30 because of the “logistical changes required”.
The women’s 20km race walk on 20 September begins at 07:30, but the men’s event on the same day is scheduled for 09:50.
When Tokyo hosted the summer Olympics in 2021, the marathon and race walking events were moved 800km north to Sapporo because of its cooler conditions.
Despite the World Championships taking place later in the year, when temperatures are expected to be lower in Tokyo, conditions have remained similar to mid-summer.
Japan has endured its hottest summer since records began in 1898, with temperatures 2.36C above average.
World Athletics president Sebastian Coe admitted earlier this week that athletes would inevitably face “heat challenges”.