A French prosecutor is investigating Takeda, who is reportedly linked to about $2 million in payments in 2013 before and after the IOC picked Tokyo ahead of Madrid and Istanbul to stage the games.
The brewing scandal is a major blow to Tokyo's preparations, which IOC President Thomas Bach has called "the best" in Olympic history.
The Tokyo Olympics open in 18 months with Japan spending at least $20 billion to prepare.
At a packed news conference Tuesday at the JOC's office, Takeda said little in a brief seven-minute statement.
Dressed in a dark suit, Takeda did not take questions and said: "I'd like to clear the allegation against me, and I will cooperate fully with French authorities."
The International Olympic Committee has backed Takeda and says he has the presumption of innocence.
He testified with an IOC ethics commission on Friday. The IOC has not commented on details.
The 2016 Rio de Janeiro Olympics were also sullied by corruption scandals. Carlos Nuzman, the head of those games, resigned afterward accused of vote-buying.
There was some speculation Takeda might use his brief address to step aside, at least temporarily.