According to the organizer, the accident must have occurred on Thursday afternoon.
The bus must have come into contact with a visually impaired pedestrian at a pedestrian crossing.
Toyota, which has developed the self-driving buses, together with the organizer must have decided to take the buses out of service during the investigation.
"We deeply regret those who were injured.
We are cooperating fully with the police in this matter ", the company writes in a statement.
Neither Tokyo 2020 nor Toyota have named the victim, but according to local media, it is the Japanese judoka Aramitsu Kitazono who was involved in the accident.
The 30-year-old fell to the ground and will need two weeks of rehabilitation for the injuries.
Kitazono would have gone to the match on Saturday, but has resigned.
The Japanese newspaper Asahi Shimbun writes that the bus stopped automatically in front of the pedestrian crossing, but that the two people in charge of the bus pressed the start button again when it thought the man had discovered the bus.
Five passengers were on board the bus and none of them were injured.
Thousands of athletes live in the Paralympic village during the Games and the self-driving buses were also used in the Olympic Village during the Olympics.