Japanese officials have been cleared of any wrongdoing in connection with a 2.8 million Singapore dollar payment (1.55m euros; $2.05m) made to a consultancy firm.
French prosecutors said they were investigating the sum in May this year as part of a corruption inquiry, BBC reported on Thursday.
But a Japanese panel found the payment did not break any Japanese laws.
The payment had been linked to the son of the ex-world athletics chief Lamine Diack, who was a member of the International Olympics Committee at the time.
Both Lamine and his son, Papa Massata Diack, are already under investigation in France. Both deny ever receiving money in connection with the Japanese bid, while Japanese officials say the payment was for consultancy services.
The payment from bid executives was made to Black Tidings, a company led by an associate of Papa Massata Diack.
"The investigation team concludes that it does not form any crime under the penal code of France, and furthermore, that no violation of the IOC code of ethics can be found," the report said.
"What was most important for the team was to probe whether the bid committee in fact bribed someone," one of the panel members, Yoshihisa Hayakawa, said.
"We think the investigation cleared the group of any suspicion in this regard."
However, he said the probe had limitations, and was unable to interview either the Diacks or the head of the consulting company, which has since ceased trading. He said the panel had "done all we can within our ability".
Japan's bid was ultimately successful, defeating Istanbul and Madrid in the process.
French prosecutors widened their corruption investigation into athletics earlier this year to include the bidding and voting process for both the 2016 and 2020 Olympics.
Lamine Diack was arrested in 2015 on corruption and money laundering charges, over allegations he took payments for deferring sanctions against Russian drugs cheats.
Papa Massata, who was employed by his father as a marketing consultant for the IAAF, is also under investigation, and a warrant for his arrest was issued by Interpol. He lives in Senegal.
He said both he and his father are innocent of any wrongdoing.
