They were involved in the loading of a passenger ferry, Clann Na nOilean, onto a large ocean-going freight carrier in the harbour.
A sling, which was being used to lift the ferry onto the cargo ship, snapped and the ferry fell 12 metres (40ft) into the water.
The three men were treated at the scene before being taken to hospital by ambulance. Their injuries are said to not be life threatening.
Galway Harbour Master Brian Sheridan said the Harbour Board is trying to establish why the three local men were on board the passenger ferry when it was being loaded onto the cargo ship.
It is routine practice for them to have left the boat before the lift began, he said.
The Health and Safety Authority has begun an investigation into the incident.
All further work on the removal of two passenger ferries at the docks has now been suspended.