A World War II-era ship painted with hundreds of penguins sank in Wellington harbour overnight.

The privately-owned Sealion was previously classified as "non-seaworthy" and had been relying on four pumps to keep it afloat.

Wellington regional harbourmaster Grant Nalder said the ship was not in the best of health.

"Yesterday there was a problem with one of those pumps and it appears water overwhelmed the other pump, so she ended up under the water instead of on top of it."

The iconic Sealion ship has been described as not being in the best of health. Photo / Supplied

Nalder said the large timber boat had many small gaps between the planks, which would have let in a fair amount of water.

"It seems the water came in the back of the boat, the stern, near the engine room, and it tilted. Once it started tilting, it just took on more water."

Nalder said the owner was in Nelson and has been informed of the ship's fate.

A caretaker was on board the ship and had alerted Nalder there was a problem with the pumps, but didn't think it was "too bad".

"Then he got off when he decided it wasn't going to end well and she went down quite quickly," Nalder said.

The privately-owned Sealion was previously classified as "non-seaworthy". Photo / Supplied

The boat was recently shifted from Queen's Wharf to Glasgow Wharf near the Bluebridge ferry terminal.

Nalder said there was a small amount of fuel coming out of the ship since it sank.

Divers have inspected the hull and contractors have been removing floating debris, ropes, and timber.

"Our primary goal at the moment is keeping the area safe. We'll work with the owner about getting it removed."

Contractors have been removing debris from the water. Photo / Supplied

 

- Georgina Campbell, NZ Herald