Takeda, 71, said he had cooperated with a judge at a hearing in Paris.
The indictment by the French magistrates does not automatically trigger a trial. However it means there are grounds for further inquiries.
French investigators are looking into a suspect payment of nearly two million euros made before Tokyo was chosen ahead of Madrid and Istanbul in 2013 to host the 2022 Olympics.
The French investigation, launched in 2016, relates to two payments made to a firm linked to the son of the former head of the International Association of Athletics Federations.
The payments were made in two stages, before and after the International Olympic Committee (IOC) vote that decided the host city.
France is investigating the case because funds involved might have been laundered in France.
Takeda represented Japan at the 1972 and 1976 Olympics. He coached the Japanese equestrian team at the 1984, 1988 and 1992 Olympics before becoming chef de mission at the 2002 and 2004 Games.
A spokesperson for the IOC said Friday it was monitoring the situation. "Mr Takeda continues to enjoy the full presumption of innocence," the spokesperson said.