Mr Inose said that from now on he would campaign "strictly in accordance with the IOC rules".
BBC: Tokyo governor in apology over Olympics comments
Naoki Inose, who is chairman of Tokyo's Olympic bid committee, made the comments in an interview in New York.
Mr Inose replaced outspoken predecessor Shintaro Ishihara, who resigned late last year to contest Japanese general elections in December 2012.
Mr Inose said his remarks had been "inappropriate".
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