Dozens of sailors were rescued from the HMNZS Manawanui in October after it struck a reef, burst into flames and finally sank south of Samoa's most populous island Upolu.

One of just nine commissioned ships in New Zealand's small naval fleet, the Manawanui had been dispatched to map the ocean floor.

A military court of inquiry on Friday found the survey vessel had been scuttled because its "autopilot was not disengaged when it should have been".

"Remaining in autopilot resulted in the ship maintaining a course toward land, until grounding and eventually stranding."

Crewmembers noticed the ship had veered off course and tried to change direction, believing they had lost control due to a "thruster control failure".

But they forgot to check if the autopilot had been disengaged first, the tribunal found.

Rather than steering away from danger, the ship "started to accelerate towards the reef".

Defence Minister Judith Collins said the debacle had "really knocked Navy for six".

"It was a terrible day. The navy and the defence force are not shying away from this.

"It was extremely disappointing. But that's what has happened."

The shipwreck settled on a stable section of reef some 30 metres (98 feet) below the surface.

It was carrying 950 tonnes of diesel when it sank, stirring fears of an oil slick that could kill wildlife and taint crucial food sources.

New Zealand's navy has said previously that the main fuel tanks appeared to be intact.

Salvage crews were working to retrieve the fuel without major leaks.

No one died in the incident, although a small number of sailors suffered minor injuries.