The questioning of Tsunekazu Takeda, who led the successful bid, and several other people involved in the bidding, was voluntary and carried out at the request of the French authorities, Kyodo said.
Takeda and the others denied doing anything illegal, the report said.
The Tokyo prosecutors' office and the JOC declined to comment on the report when contacted by Reuters.
French prosecutors last year announced an investigation into more than $2 million of payments made by the bid committee to the consultancy, Black Tidings.
Black Tidings is headed by Ian Tan Tong Hon, who is known to be friends with Papa Massata Diack, son of disgraced former international athletics chief Lamine Diack.
Japanese officials repeatedly said the payments had been legitimate consultant's fees, and a panel commissioned by the JOC said in September it had found that the payment was legitimate.
Tokyo 2020 organisers have been grappling with a list of headaches including soaring costs and calls to change venues.
The country club that will host the golf tournaments has come under fire for its policy of barring women from becoming full members, and a trade show group is calling on Tokyo to find a new location for the international media centre.
(Reporting by Chris Gallagher; editing by Sudipto Ganguly)
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