The carcass of a critically endangered Bryde's whale has been found by boaties off Waiheke Island's Cactus Bay.

The whales live on the eastern coast of the North Island, particularly in the Hauraki Gulf, and there are only around 100 of the species remaining.

Craig McIvor was on board the Free Flyer owned by Bruce and Gabrielle Young on Sunday evening when they spotted what they initially thought was the hull of an upturned yacht.

Further investigation revealed it was the underside of a dead whale.

McIvor says it was about 15 metres long and it appeared to have suffered a few shark bites. The group immediately informed the Department of Conservation.

Department programme manager of biodiversity Phil Brown says by the time the two department boats went out on Monday morning to secure the carcass it had floated to just off Tiritiri Matangi Island.

The whale was towed to Motuihe Island where specialised vets yesterday performed a post mortem.

Brown is awaiting the results of how the whale died but has confirmed it is a Bryde's whale.  

He says Bryde's whales spend a lot of time near the surface making them vulnerable to being hit by ships.

"These whales are being killed at an unsustainable level," Brown says.

In an effort to protect them he says the department is talking to the commercial shipping industry about slowing the ships down.

He says there are a number of other places around the world where this happens so many of the shipping operators are used to doing it.

The last Bryde's whale to die after being hit by a passing ship was on the opening night of the Rugby World Cup, just four months ago. It was towed to the Coromandel.

After completing the post mortem the whale will either be buried or sunk using weights, Brown says.

Phone 0800DOCHOT or 0800-362-468 with any sighting of a whale.

- © Fairfax NZ News