According to Le Monde, Takeda, a member of the International Olympic Committee (IOC) who led the Tokyo bid, is suspected of authorising the payment of bribes in order to help the Japanese capital secure the hosting rights for the 2020 Games.
The 71-year-old was indicted by the national financial prosecutor’s office in Paris last month, Reuters reported.
In a statement, the IOC Ethics Commission, which is holding a meeting here in Lausanne today, had opened a file on Takeda but said the Japanese official "continues to enjoy the full presumption of innocence".
Takeda is being investigated for "active corruption", according to Le Monde, regarding 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.
The account holder has been closely tied to Papa Massata Diack, 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, with authorities in France suspecting corruption or money laundering by an unknown person.
Tokyo, the winner of the first round of the 2020 vote, defeated Istanbul by 60 votes to 36 in the second ballot.
Madrid were eliminated in the first round.
An investigation team, established by the JOC, cleared Tokyo 2020 over the controversial payment in 2016, dismissing allegations it was used as a bribe as Lamine Diack was a voting IOC member at the time of the 2013 vote.
Takeda was questioned by Japanese prosecutors in 2017 in relation to the payments.
Today's revelation represents another considerable blow to the IOC and Tokyo 2020, who have denied any wrongdoing contributed to their triumph at the 2013 Session in Buenos Aires.
"The IOC is ‘partie civile’ in this investigation and has been in close contact with the French judicial authorities," the IOC said in its statement.
"The IOC Ethics Commission has opened a file and will continue to monitor the situation - and is meeting today.
"Mr Takeda continues to enjoy the full presumption of innocence.
"These allegations refer to events before the IOC introduced far reaching reforms.
"With the reforms of Olympic Agenda 2020 the IOC reinforced its code of ethics and introduced an approved list of consultants.
"In order to be on the list the consultants have to declare that they respect the strict IOC rules on governance and ethics, and in particular anti-corruption.
"Candidate cities can only hire consultants that are on the list.
"As for the former President of the IAAF, Mr Diack no longer holds any position within the IOC.
"In 2015, the IOC provisionally suspended Mr Diack who then within 24 hours himself resigned as an honorary member.
"We continue to keep close contact with the judiciary authorities and the IOC President has even sent a letter to the President of Senegal to ask him for full cooperation, something to which President Macky Sall agreed."
Takeda, the great-grandson of Emperor Meiji and who represented Japan at the 1972 and 1976 Summer Olympics, is considered a well-respected IOC member and Japanese sports official.
He has served as head of the IOC's influential Marketing Commission since 2014 and was granted an age limit exemption to remain a member beyond his 70th birthday last year.
It means he will continue to serve on the IOC after Tokyo 2020.
The JOC were also set to extend the age limit so Takeda can stay on as President until the end of the 2020 Games.
The IOC Marketing Commission are scheduled to meet in Lausanne next Saturday (January 19) but it is unlikely Takeda will attend given today's announcement.
insidethegames has contacted Tokyo 2020 for comment.