The World Athletics Championships in Doha, Qatar were marred by images of athletes collapsing during the midnight marathons, prompting IOC president Thomas Bach to demand a change in location for the Olympics.
Temperatures in Tokyo during July and August regularly top 30°C, with high humidity also a worry.
Tokyo governor reluctantly accepts IOC move of Olympic marathon
"We cannot agree with the final decision, but the IOC has the authority to change [the location]," Koike said.
"The most important thing is to assure the success of next year’s Games. I think we must move forward. I don’t approve, but the decision can’t be avoided."
The Guardian quotes a Japanese news report which claims she called it a "painful decision, not an agreement".
Alisa Vainio of Finland is taken off on a wheelchair after the Women's Marathon
Image credit: Getty Images
Koike had previously fumed at the IOC’s decision, saying Tokyo had taken precautions to reduce the impact of the heat on athletes – including scheduling the marathon start times for 6am local time and installing mist machines.
"To choose Sapporo so suddenly… why Sapporo, who decided this?" she said.
"There was no discussion, and I have a lot of doubts about having this thrust on us. We have made many preparations and there’s no change in my thinking that it should be held in Tokyo."
Sapporo, over 500 miles away from Tokyo, is the capital of the mountainous northern Japanese island of Hokkaido.