Tokyo 2020 CEO Toshiro Muto's comment on the case was his first since news emerged last month that Takeda had been questioned in Paris and placed under formal investigation for suspected corruption in Japan's successful bid to host the Games.
Takeda, head of the Japanese Olympic Committee since 2001, is also a vice president on Tokyo 2020's executive board.
"Mr. Takeda is saying that he's completely innocent so when we are at this stage, going beyond that, we can't take action at this point in time when he's asserting his innocence," Muto told reporters on Friday after a working-level meeting with the International Olympic Committee (IOC).
French prosecutors have been investigating a multi-million dollar payment made by the Tokyo bid committee to a Singapore consulting company. The prosecuting judge now suspects Takeda of paying bribes to secure the winning bid, a judicial source told Reuters.
Takeda, who was president of the Tokyo 2020 bid committee, has denied any wrongdoing, saying that there was nothing improper with the contracts made between the committee and the consultancy and that they for legitimate work.
The investigation is an embarrassment for the IOC, which has been trying to clean up the bidding process around the Olympic Games after a series of corruption allegations and increased spending by host cities.
The IOC's ethics commission has opened an ethics file on Takeda, who is also an IOC member and chairs its marketing commission.
"We are expecting the inquiry to progress and at some point in time a judgment will be rendered. At this point in time we cannot anticipate where it is heading," Christophe Dubi, Olympic Games executive director at the IOC, told the same briefing.
"But the main point is this organisation has evolved and keeps on evolving," he said, noting that the IOC had enacted measures in its Agenda 2020 reforms to improve governance in several areas including the bidding process.
"The whole process itself is far more transparent," he said.
On Thursday, public broadcaster NHK reported that Games organisers have decided to cut the number of spectators for the sailing events at Tokyo 2020 over tsunami fears.
Organisers have reduced capacity at the events off Enoshima island by a third so that spectators could be quickly evacuated to higher ground in the event of a tsunami.
Japan is one of the most seismically active countries in the world and one of the Games' biggest challenges is to be prepared for possible disaster.
(Reporting by Chris Gallagher; Editing by Amlan Chakraborty)
