Security sources said the preliminary conclusion from a police forensics investigation was that the damage was caused by three rocks thrown at the bus.
Passengers on the bus reported hearing the sound of gunfire as it passed through the Curicaca neighbourhood just north of Olympic Park and two windows were shattered.
"Even if the report concludes it was stones, that is totally unacceptable," said Rio 2016 spokesman Mario Andrada.
Military police were stationed along the road where the incident occurred between the Games basketball venue and the main Olympic Park, security sources said.
Concern has mounted over a series of robberies during the Rio Games. Police also were investigating a stray bullet that struck a temporary media room at the equestrian centre on Saturday.
Local media reported that a Belgian judoka was assaulted and robbed on Tuesday near the famous Copacabana beach.
A Reuters photograph taken in the first moments after the bus incident showed a small hole, about the width of a finger, in one of the windows.
"We were shot at. I mean we could hear the report of the gun," said Sherryl "Lee" Michaelson, a retired U.S. air force captain who is working for a basketball publication in Rio.
(Reporting by Daniel Flynn; Editing by Jeffrey Benkoe)
