French prosecutors said in May that they were investigating the 2.8 million Singapore dollar (1.8 million euros, $2 million) payment to a Singapore-based consultancy.
Shortly after, the Japanese Olympic Committee set up an investigative panel of three lawyers to look into the payment, which has been linked to a son of disgraced ex-world athletics chief Lamine Diack.
Diack, whose son Papa Massata Diack has denied receiving the money, was an International Olympic Committee (IOC) member at the time.
"The investigation concludes that (the bid committee's deals) are not in violation of any of the laws of Japan," the panel's report said.
"In addition, 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."
Japanese officials have consistently denied wrongdoing and have said that the payment was for consulting services related to the bid.
"What was most important for the team was to probe whether the bid committee in fact bribed someone," Yoshihisa Hayakawa, the lawyer who led the investigation, told reporters.
"We think the investigation cleared the group of any suspicion in this regard."
But Hayakawa stressed the probe's limitations and its inability to interview key people -- such as the Diacks and the head of the now defunct consulting company.
"As a team without authority for compulsory investigation, we have done all we can within our ability," he said.
The money was sent in two tranches to the now-defunct, Singapore-based Black Tidings company, either side of the International Olympic Committee vote which awarded Tokyo the 2020 Games.
Japan beat Istanbul and Madrid in the race to host the Summer Games in the vote held in 2013. Black Tidings was headed by consultant Ian Tan Tong Han, an associate of Papa Massata Diack since the 2008 Beijing Olympics.