The men's 50km race walk will start even earlier, at 5:30am, with organisers saying they had taken medical advice into account in timetabling the events.
The scheduling decisions were taken "after discussions with medical teams and stakeholders and considering the well-being of athletes", Tokyo 2020 sports director Koji Murofushi told reporters.
Other sports, including rugby sevens, triathlon and mountain biking have also seen schedules shifted to avoid the worst of potentially blistering temperatures for the July 24 to August 9 Games.
Games organisers had already said the marathons would start "between 5:30am and 6am" after a heatwave that struck the country last summer, prompting Japanese medics to warn that running the race in mid-morning could "lead to deaths" from heatstroke.
The last time Japan hosted the Summer Olympics, in 1964, the competition was held in October to avoid the hot summer conditions.
Tokyo 2020 CEO Toshiro Muto said the possibility of extreme weather conditions, ranging from typhoons to heatwaves, was a "major issue" for the Games and International Olympic Committee chief Thomas Bach has also voiced concern.
Tokyo has considered a range of options to counteract the heat, including the adoption of daylight saving, a proposal that gained little traction.
But other countermeasures such as solar-blocking paint on roads and mobile misting stations are planned, with Muto admitting that there had been a knock-on impact on the $12.6 billion budget.
There are plans for a special centre to monitor extreme weather and warn of potential emergencies including the risk of heatstroke, even recommending evacuation if necessary.
Last summer, Tokyo sweated through several deadly heatwaves and Japan was also battered by a series of typhoons that caused death, destruction and delay.
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