The bus carrying 75 Czech tourists, some schoolchildren, was travelling from Spain to the Czech Republic when it was hit on Saturday night.
Two shots smashed the front and rear windows, Alex Perrin, a prosecutor in the Drome region, said.
Le Dauphin Libere newspaper said more police were stationed on bridges over the A7 in case of repeat incidents.
It is believed the attacker was using a hunting rifle to target the bus from a bridge over the A7 near Saulce sur Rhone, roughly halfway between Lyon and Marseille.
Among the six people injured by broken glass was a child, Mr Perrin said.
One passenger suffered a serious eye injury, he added.
"We don't have any reason to believe this bus was targeted instead of any other," Mr Perrin said.
No-one has yet been arrested.
Six people were when shots were fired at a tourist bus on the A7 motorway in south-east France, police say.