Tsunekazu Takeda is being investigated by French prosecutors who are looking into claims of a 2m Euros bribe was paid to secure Tokyo's winning bid.
Tokyo was awarded the Games in 2013, beating Madrid and Istanbul.
Takeda's tenure ends in June and the Japanese government has always insisted its Tokyo bid was clean.
The company to which the payment was made is linked to the son of former world athletics chief Lamine Diack, who was a member of the International Olympic Committee when it awarded the Games to Tokyo and is the subject of corruption allegations being looked at by French investigators.
Takeda is a veteran Olympics official who competed as a show jumper in 1972 and 1976.
[Source: RNZ]
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