Crews were called out at just before 3am to reports of a 360 excavation digger involved in fire inside a 7,000 tonne ship hold.
Humberside fire service said a small quantity of biomass fuel wooden pellets was involved in the fire underneath the digger.
The team used two hose reel jets, two main jets and extension ladders to bring it under control.
The digger was removed onto the dockside by crane, with the help of security staff.
Powerful water jets were then used to fully extinguish the fire once the digger was on the dock side.
A brigade spokesperson said no injuries have been reported. The cause is still being investigated.