The fortunes of the HMNZS Wellington and its crew have changed significantly after sailing through a nightmarish storm.

After battling through hurricane-strength winds and 14 metre waves in a storm which the ship's captain, Lieutenant Commander Phil Rowe, described as his worst in his 28-year Navy career, the ship has taken anchor in Stewart Island's sheltered Port Pegasus.

The ship, which also has Conservation Minister Nick Smith, Metservice and Conservation Department staff and businessmen Gareth and Sam Morgan on board, was forced to turn back from its voyage to the subantarctic islands and seek shelter.

Moored in the stunning harbour, the crew entertained themselves  yesterday by fishing and working out. A barbecue and quiz were held tonight. 

Smith and the non-Navy staff were ferried ashore to go tramping on Bald Cone and visit Broad Bay, one of Stewart Island's endangered sea lion haunts, though there were  only one sea lion and three penguins to see.

"It felt truly bizarre to go from a Southern Ocean environment of 14-metre swells to the millpond of Pegasus Inlet where the wave height wouldn't have been 14 millimetres," Smith said.

"It was truly a wild storm and I never expected to see waves higher than any of the buildings in Nelson." The most unnerving moment "was when the captain advised me that we needed to turn back but that we couldn’t actually make the turn until the sea calmed, simply because the ship was not fit to take that scale of waves on the beam".

"The look on the captain's face was cool as a cucumber until there was an alarm for a fire which later turned out to be a fire extinguisher that had been thrown out of its catch. It was the only time that I thought I was in any danger."

Smith joked he would be approaching Nelson fishing companies "for a share of the quota given the contribution I've made to feeding the fish".

 Rowe said the ship had come through largely unscathed from the storm and that he was pleased with the way the ship and crew had handled it.

"It was interesting to gauge the reaction of the ship's company and the other people on board, but the ship did really well to come through that, as did the ship's company. We lost a few to sea sickness, but we get that all the time."

Hearing the smoke alarm go off after it was triggered by a dislodged fire extinguisher was unfortunate "but the guys are trained for it and the adrenalin kicks in and that takes over any seasickness". 

It was not unusual to have such day-to-day extremes in the Navy, he said. 

"Thirty six hours ago we are facing 14-metre seas and 70 knot winds and now you look round the ship and you'd think the ship hadn't been through that. We're just doing what we do."

Smith said the Stewart Island excursions were an unexpected upside to being forced to turn around. 

"I've always had an ambition to get down to this bottom corner of Stewart Island and there are ambitions by some for marine reserves in this area… It was also a good experience today to meet my first New Zealand sea lion, having signed out tens of thousands of letters about their survival during my political career."

DOC's South Island conservation service manager Brent Beaven described the area as one of New Zealand's most unique and pristine.

The ship is waiting for a second storm to pass before resuming its journey to the subantarctic islands.