A full inquiry will be launched into the latest breakdown of the Navy's newest ship, the 85-metre offshore patrol vessel, HMNZS Otago.

An electrical fault in one of its two engines has cut short a mission to the Auckland and Campbell islands, 700km south of New Zealand.

The fault meant the engines had to be operated manually, Defence Minister Wayne Mapp said.

VIP guests on the ship included the Governor General, Sir Anand Satyanand, and cabinet minister Kate Wilkinson are transferring to Otago's sister ship, HMNZS Wellington, today.

The ships encountered heavy seas on the trip to the sub-Antarctic islands and last night Otago was anchored in Perseverance Harbour at Campbell Island.

Otago was carrying scientists for a three month expedition to study the ecology, archaeology and human impact on the island.

Sir Anand and Ms Wilkinson will head 270km northwest to Auckland Island on the HMNZS Wellington before returning to Dunedin on Sunday.

Crew on Otago have restarted the faulty engine and the ship is to head back to the Devonport naval base in Auckland for permanent repairs.

One aim of the mission was to test the capabilities of both ships in the challenging conditions of the Southern Ocean, the navy said.

Dr Mapp said the fault, the latest in a series of faults to dog both offshore patrol vessels, was frustrating but repairs would covered under warranty.

"There will be a full inquiry undertaken because the next time the ships go out together we want them to be both fully operational.

"The navy is convening an inquiry, essentially a technical review which will include an independent technical expert. We do want to get to the bottom of all these issues and make sure they are all solved so these things don't occur in the future," Dr Mapp told Radio New Zealand.

Earlier this year the navy ruled out sabotage after the ship returned to Auckland soon after leaving Devonport on its first deployment out of New Zealand.

It was heading to the Pacific Islands when the fuel was found to be contaminated with water.

The ship was part of the $500 million Project Protector which saw seven new ships added to the fleet, including Otago and Wellington, the multi-role ship HMNZS Canterbury and four inshore patrol vessels.

The Government negotiated an $85 million settlement with the ship builders, mainly for problems which arose on Canterbury, but also for lesser problems on the other ships.

- NZPA