Crews from Point Cook, Hoppers Crossing, Werribee and Truganina had to ferry water to the scene from a nearby dam as there was no mains water available.
Four boatsheds were destroyed but firefighters managed to bring the fire under control before the last two in the tightly-packed row of six were damaged.
The fire was reported just before 8pm last night and the last crews left the scene after midnight.
Ambulance Victoria paramedics were on scene to monitor firefighters working in breathing apparatus.
Firefighters' gear was bagged and sent off for testing for asbestos contamination as a precaution.
The Incident Controller was Station Officer Darren Miller from Point Cook.