Consultancy firm Black Tidings reportedly transferred $370,000 (£288,000/€313,000) to Papa Massata Diack around the time Tokyo was awarded the 2020 Olympic Games.
According to Kyodo News, documents show payments from the Singapore based company to a firm owned by the Senegalese.
Payments worth $2 million (£1.56 million/€1.70 million) made to Black Tidings are the subject of investigations by French authorities in relation to alleged vote buying in connection with the 2020 Olympic and Paralympic bid race.
The payments were made before Tokyo was awarded the 2020 Olympics and Paralympics at the International Olympic Committee (IOC) Session in Buenos Aires in 2013.
The holder of the Black Tidings account has been linked to Papa Massata Diack, the son of the former International Association of Athletics Federations President and IOC member Lamine Diack.
Documents reportedly show Black Tidings transferred the $370,000 to Papa Massata Diack's personal account and to his company PMD Consulting Sarl.
Payments were made from August 2013 to January 2014.
Papa Massata Diack told Kyodo News that the money received was related to a "sponsorship deal made in China".
"There is nothing to do with the Tokyo Olympics," he said.
The transfers were discovered by the International Consortium of Investigative Journalists, as well as BuzzFeed News, The Asahi Shimbun, Kyodo News and Radio France.
The findings came after analysis of leaked reports of suspicious financial activity, which have been kept by the United States Treasury Department and French authorities.
Lamine and Papa Massata Diack are at the centre of a corruption probe relating to the bid process for the 2020 Olympics and Paralympics, due to the payments made to Black Tidings.
Lamine Diack was a member of the IOC during the time of the vote and was viewed as having considerable influence over African IOC members
Both of the Diacks deny wrongdoing.
Former Japanese Olympic Committee (JOC) President Tsunekazu Takeda, chair of the Tokyo 2020 Bid Committee, is also being investigated over allegedly authorising the payments to Black Tidings.
Takeda, who denies wrongdoing, resigned as JOC President and as a member of the IOC last year after he was implicated in the scandal.
Lamine Diack was last week sentenced to two years in prison after being found guilty of corruption by a French court, related to covering up Russian doping cases in exchange for cash when he was in charge of global athletics.
The cover-up of cases allowed athletes from the country to compete at major events including the 2012 Olympic Games in London and the 2013 World Championships in Moscow,
It is unlikely that the 87-year-old will spend any time in prison after the judge told him he could "expect conditional release" due to his age.
Papa Massata, who refuses to be extradited from Senegal, was also convicted and jailed for five years in absentia.
Tokyo 2020 has been postponed until next year because of the coronavirus pandemic.