“As of today I will resign from the president's position,” Yoshiro Mori said to open a meeting of the Olympic Committee's executive board and council.
It was unclear who would succeed him.
Mori's departure comes after outcry both at home and abroad after he reportedly said women talk too much and have a “strong sense of rivalry” during a board meeting earlier this month.
After a wave of criticism, Mori, 83, apologized and retracted his remarks, acknowledging they were inappropriate and against the Olympic spirit.
He apologized again Friday as he announced he was stepping down. "My inappropriate comments caused big trouble. I am sorry," he said.
Mori added that he felt his comments were misinterpreted by the media and that he was not prejudiced against women.
“The IOC fully respects President Mori’s decision to step down and understands his reasons for doing so," its president, Thomas Bach, said in a statement later Friday.
"The IOC will continue working hand-in-hand with his successor to deliver safe and secure Olympic Games Tokyo 2020 in 2021.”
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The saga has dealt a fresh blow to the embattled games, already marred by fears around the coronavirus pandemic.
Although Japan has not suffered virus outbreaks on the scale of other major economies, such as the United States and Britain, it recently extended its state of emergency in Tokyo and other regions by another month.
The country of 126 million reported its worst one-day death toll for the pandemic Thursday with 121 new deaths and has also yet to start mass vaccinations.
Covid-19 aside, the organizing committee has also been grappling with ballooning costs and dwindling enthusiasm among the Japanese public, with nearly 80 percent saying the Olympics should be canceled or further delayed — all against the backdrop of a sudden change in leadership in the country after the departure of Prime Minister Shinzo Abe last summer.
“Japan's staging of the Tokyo Games was supposed to be about the country changing, turning outwards, reforming and projecting a more contemporary image,” said Simon Chadwick, sports academic and director of the Center for the Eurasian Sport Industry at the Emlyon Business School in France.
“However, it has been a case of triple-whammy for Japan: first the pandemic, then Abe leaving office due to illness and now Mori's resignation. Things could hardly have been worse than the situation Tokyo now faces.”
Following Mori’s remarks, hundreds of Olympic volunteers have quit and local organizers have received thousands of complaints, according to local media.
Japan’s Olympic tennis hopeful, Naomi Osaka, said his comments were “really ignorant” and Olympic champion swimmer Kosuke Hagino called them “very unfortunate.”
Several sponsors also voiced concerns.
The controversy has also put the spotlight on the sexism and gender equality that still linger among Japan's conservative, male-dominated elites.
The issue has dominated parliamentary sessions for days with the opposition urging the country’s government to take action against Mori, a former prime minister himself. A group of female opposition lawmakers wore white, in homage to the women's suffrage movement, with roses on their lapels in protest of Mori’s remarks.
Japan trails other developed nations in promoting gender equality. It stands 121st out of 153 countries in the World Economic Forum’s 2020 gender gap index, which highlights gender-based disparities around the world.
Japan’s gender gap is by far the largest among all advanced economies and has widened over the past year, the index said, with only 15 percent of senior and leadership positions held by women.
Although the younger generation is more socially progressive and more sensitive to gender equality issues, social practices are slower to change and Japan lags behind — especially in the absence of female representation in leadership positions, said Koichi Nakano, a political science professor at Tokyo’s Sophia University.
“This is precisely why Mori’s comments were so strongly rejected by the public,” he added.
“The Japanese are often reluctant to take positions on issues that are seen as political, but the negative reaction was practically unanimous on this one,” Nakano said.
But while Mori’s comments and resignation are yet another crisis that the Tokyo Games organizers have to tackle, it will likely get lost in the legacy of the Olympics faced with a pandemic, said Heather Dichter, an associate professor of sports management and sport history at the De Montfort University in the United Kingdom.
“The biggest thing that people will always talk about is how they have dealt with the pandemic," Dichter said.
“That will be what people will remember these games for.”
Arata Yamamoto reported from Tokyo, and Yuliya Talmazan reported from London.
Reuters contributed to this report.