The accident occurred last month during an engineering possession near to Port Glasgow station.
One worker became trapped between the wagon and a track panel which had previously been set down on the railway by a second crane. Both cranes were being used as part of the renewal of a section of track within the possession.
The track worker who was trapped had to be freed by the emergency services and was subsequently treated in hospital for his injuries.
The RAIB will now examine the circumstances of the accident and publish an incident report.