Inose, who is also chairman of the bid committee, was quoted in the New York Times last weekend suggesting that Istanbul is less developed and less equipped to host the games than the Japanese capital.
In an interview conducted in New York, Inose said "For the athletes, where will be the best place to be? Well, compare the two countries where they have yet to build infrastructure, very sophisticated facilities".
Inose was also quoted saying "Islamic countries, the only thing they share in common is Allah and they are fighting with each other, and they have classes."
Tokyo is vying with Istanbul and Madrid for the right to host the 2020 Olympics. The International Olympic Committee will select the host city by secret ballot at its assembly in Buenos Aires, Argentina on Sept 7.
The governor's comments appear to break the IOC's rules prohibiting bid cities from commenting on rival candidates. The remarks could lead to a reprimand or warning from the IOC ethics commission.
Japanese Olympic Committee President Tsunekazu Takeda has received an email seeking confirmation of the facts of the matter from the IOC, Kyodo News agency reported today.