Tsunekazu Takeda will resign as President of the Japanese Olympic Committee (JOC) following bribery allegations linked to the successful bid from Tokyo 2020.
Reports that he would step down initially emerged last week, with the official now announcing his resignation formally at a news conference in Tokyo.
The 71-year-old, the son of Prince Tsuneyoshi Takeda and great-grandson of the 19th century Emperor Meiji, will also leave his role as an International Olympic Committee (IOC) member, where he was chair of the influential Marketing Commission.
He had been a member of the IOC since 2012.
According to the Japanese news agency Kyodo News, Takeda, while denying the allegations, apologised for the disruption he had caused.
He will officially depart as JOC President on June 27 when his term ends.
"It is most appropriate to leave the JOC to younger leaders as we await the Tokyo Olympics and Paralympics, and have them open up a new era," he reportedly said following a meeting of the JOC's Board," he said.
"I have not committed any wrongdoing.
"I will strive to prove my innocence."
Takeda's position first came under scrutiny in January after it emerged he had been indicted in France on corruption charges.
Tadeka is suspected of authorising the payment of bribes in order to help Japan's capital secure the hosting rights for the 2020 Olympic and Paralympic Games.
At the time French newspaper Le Monde reported that Takeda is being investigated for "active corruption".
It concerns payments worth $2 million (£1.5 million/€1.75 million) made to Singaporean company Black Tidings before Tokyo was awarded the 2020 Olympics and Paralympics at the IOC Session in Buenos Aires in 2013.
The account holder has been closely tied to Papa Massata Diack, the son of the disgraced former International Association of Athletics Federations (IAAF) President Lamine Diack, who is currently being held in France and facing corruption charges.
It is alleged the payments were directed to the elder Diack, an influential voting IOC member at the time.
Authorities in France suspect corruption or money laundering by an unknown person.
Tokyo defeated Istanbul by 60 votes to 36 in the second ballot.
Madrid had been eliminated in the first round.
Takeda has always protested his innocence and was initially backed to stay as JOC President despite the controversy.
At the start of February, Tokyo 2020 chief executive Toshirō Mutō claimed there was no reason for Takeda to step down and Takeda himself initially appeared resistant to leave.
He at first chose not to self suspend himself from the IOC, in contrast to other members who have found themselves embroiled in similar cases.
According to Kyodo News, the catalyst for Takeda's decision to step down reportedly came after IOC President Thomas Bach turned down an invitation to attend one-year to go celebrations for Tokyo 2020 on July 24, for fears of being associated with Takeda.
Just two weeks ago Takeda was re-elected as vice-president of the Olympic Council of Asia (OCA) after the organisation's Ethics Committee cleared him of any wrongdoing.
Amid this latest revelation it is now unclear whether he will remain in that position and insidethegames has contacted the OCA for comment.
Takeda had been JOC President since 2001 and was serving his 10th term.
The alleged payment of funds was first reported in 2016 but a Japanese probe at the time later concluded that there was no illegality.
In a statement sent to insidethegames the IOC said they "greatly respect" Takeda's decision to step down.
"The IOC takes note with the greatest respect of the decision taken by Mr Takeda to resign as an IOC member," they said.
"Our respect of this decision is even greater because he took this step to protect the Olympic Movement while the presumption of innocence, on which the IOC insists, continues to prevail."
It is now less than 500 days until the Ceremony of the 2020 Olympic Games in Tokyo on July 24 next year.