The panel, commissioned by the Japanese Olympic Committee (JOC), concluded in its report that the payments to Singaporean firm Black Tidings were not a bribe.
Japan's hosting of the Summer Games has been mired in setbacks, including an overhaul of the stadium design, which was abandoned in response to public anger over soaring costs, and plagiarism allegations over its original logo.
"I believe the suspicion of bribery by the bid team has been cleared," said lawyer Yoshihisa Hayakawa, who headed the investigation.
Tokyo bid team's executives had no knowledge of the link between Ian Tan Tong Han, the head of Black Tidings, and Papa Massata Diack, the son of disgraced former international athletics chief Lamine Diack, the panel, comprised of two lawyers and a certified public accountant, concluded.
Diack is facing charges in France for corruption at the IAAF, athletics' governing body, the panel concluded.
While the $2 million fee is double the average the Tokyo bid team paid to other such consultants, Tan, a successful lobbyist, deserved the fee, the panel found in its report.
The investigators were unable to speak with Tan, Diack or his son, Papa Massata Diack, Hayakawa said. The team conducted hearings with members of the bid team and analysed relevant documents, the report said.
The investigation panel does not know exactly how Tan spent the money or whether he transferred it to Diack or his son, Hayakawa added.
Even if money was transferred from Tan to Diack, such transfers would not be considered bribery as the bid team was not aware of the transfer or the tie between the two.
(Editing by Angus MacSwan)
