The Waikato Regional Council says a 15-metre boat floating in the Tairua River had four tonnes of mussels stuck to its hull when it was pulled out of the water.
They say the ship has been docked in the harbour for over a decade but recently its owner stopped maintaining it.
The council's maritime services manager Nicole Botherway said the sheer weight of the shellfish put the boat at risk of sinking, and becoming a major hazard for other boat users.
"The vessel itself is about steel hulled and it's around about twenty tonnes just in vessel, so yeah they do collect quite a lot but obviously that's a very large build-up over a long period of time where the owner has just basically done nothing about it."
She said the council had to bring in a crane to get the boat out of the water - and they would be seeking costs from its owner.