The interior ministry said a heated argument escalated into a fight after the policeman told the driver he was blocking the road.
Other bus drivers joined the fight by attacking the policeman, who then allegedly shot the driver in the groin.
Egypt has seen a series of allegations of police brutality in recent months.
In a statement, the interior ministry said the officer Ahmed Samir Nassar had been suspended and referred for prosecution over the incident.
It added that security forces took the injured driver to hospital after the shooting.
The incident is believed to have happened earlier this week.
Photographs published by Egypt's Tahrirnews website showed what appeared to be the driver lying on a stretcher in hospital, covered in blood.
In February, there was a protest outside the Cairo security directorate after a policeman reportedly shot dead a driver in a street in an argument over a fare.
There were also riots in Ismailia and the southern city of Luxor after at least three people died in police custody in a single week in November.
An Egyptian police officer has been suspended and is under investigation for allegedly shooting and wounding a minibus driver in the capital Cairo.