Abdulcelil Oz, the governor of Trabzon, said the driver appeared to have been hit by a bullet, changing an earlier statement in which he claimed the driver was believed to have been hit by a stone.
"The latest situation is that it appears to be a gun," Oz said. "It is too soon to say anything definite, but it appears to be a type of bullet fired by a rifle."
Fenerbahce TV maintained the bus was attacked by an assailant with a shotgun. It said security officers on board quickly took control of the bus and safely stopped it after the driver was hit, averting an accident. None of the players were hurt.
The attack came after the team's 5-1 win over the Black Sea side Caykur Rizespor in their Turkish Super League game.
The players were travelling from the city of Rize to the airport in the neighbouring city of Trabzon, to return to Istanbul.
Oz said an investigation was launched and vowed to catch the assailant.
President Recep Tayyip Erdogan and Turkish clubs condemned the attack.Suggest a correction