Haruyuki Takahashi, 78, is accused of taking payments totalling $380,000 (£315,000) from a high street business-suit retailer.
The retailer, Aoki Holdings, was an official partner of the Tokyo 2020 games.
According to Reuters news agency, Mr Takahashi has not immediately responded to requests for comment.
Documents from the Tokyo Prosecutors Office seen by AFP news agency reportedly accuse him of taking sums of money on the understanding that they were "thank-you" payments for beneficial treatment he gave to Aoki Holdings.
They allege that more than 50 transactions occurred between October 2017 and March 2022 with money send to the bank account of a company run by Mr Takahashi.
According to local media, officials have been looking into whether or not past payments received violated a law forbidding public servants from taking money in relation to their role.
Legal officials also revealed that a former chairman and two other executives of Aoki Holdings had been arrested in connection with the case.
The company has released a statement saying that it is fully cooperating with prosecutors.
A former executive at one of Japan's largest advertising agencies, Dentsu Inc, Mr Takahashi became a member of the Olympics organising committee in 2014.
While it has mostly shuttered operations the committee does maintain a financial presence to deal with accounting issues.
-- Courtesy of BBC News