The accident occurred on the Midland Mainline in Barrow Upon Soar, Loughborough, Leicestershire at 6.32, according to British Transport Police.
The train driver sustained deep lacerations to his legs and was transferred to hospital, but his injuries are not thought to be life threatening.
Six passengers were onboard at the time of the crash, with one minor injury reported. The driver of the ballast truck had to be cut free by a fire crew.
The train was the 0613 Nottingham to Norwich service and remained upright despite being derailed by rubble from the bridge.
The Rail Accident Investigation Branch (RAIB) is currently on scene and conducting a preliminary investigation, with British Transport Police and Network Rail officials also in attendance.
The identity of the contractor whose ballast truck hit the bridge is yet to be revealed.
Network Rail said the Midland Main Line was likely to be closed at the crash location for at least the rest of the day.