The Guardian newspaper reported on Wednesday that the Tokyo team had made the payments to a Singapore bank account it said was linked to Papa Massata Diack, son of disgraced former IAAF President Lamine Diack.
Japanese chief cabinet secretary Yoshihide Suga told a news conference that he was unaware of the newspaper report.
"I am confident that our bid was conducted in a clean manner," Suga said, adding that should Tokyo be approached by French authorities on the matter, it would cooperate.
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An aerial view shows the planned construction site (C) for the new National Stadium for 2020 Tokyo Olympics and Paralympics, in Tokyo, in this photo taken by Kyodo July 17, 2015

Image credit: Reuters

Diack is under a French police investigation for corruption at the IAAF, athletics' governing body. His son, believed to be in Senegal, declined to comment to the Guardian because of the investigation, the paper reported.
The International Olympic Committee (IOC) said on Wednesday it had been in touch with French magistrates. An IOC spokesman said the group's ethics and compliance officer would continue to be in contact with French authorities to clarify any alleged improper conduct, while French prosecutors declined to comment.
Hikariko Ono, spokeswoman for the Tokyo Organising Committee for 2020, which is different from the bid committee that won the right to host the games, said the committee believes Tokyo won because it presented the best bid. Yasuhiro Nakamori, spokesman for the Japan Olympic Committee, agreed.
"We have not been asked any questions by the IOC on this matter," he added. JOC chief Tsunekazu Takeda was out of the country until the weekend.
Japan, which won the right to host the games over Istanbul and Madrid in 2013, has been beset by a number of woes over the Games, including scrapping its original design for the centrepiece Olympic stadium, which has delayed construction.
Last month it selected a new games logo after its previous one was withdrawn due to allegations of plagiarism.
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