A seriously injured cruise ship passenger was winched off overnight after breaking her back.

The Rescue Co-ordination Centre said the night-time mission happened in the Cook Strait, 80km southeast of Wellington on the Legend of the Seas.

The ship is on the final leg of a 15-day round New Zealand trip, which left Brisbane on January 15 and is due back in Australia on Sunday.

A spokesman said an emergency call was made at 12.30am.

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A rescue helicopter was sent to fly the woman to the capital.

The Life Flight Westpac Rescue Helicopter used night vision googles to reach the moving ship before a medic and gear were winched to the deck to stabilise the woman and winch her up.

Helicopter crewman Mike Beausoleil described the night-time winch a challenging mission as the helicopter hovered over the large cruise ship in the dead of night.

"I would call it one of the most challenging winch scenarios I've done because it was at night over water on a moving vessel."

He said fortunately conditions were good after gale-force winds pounded the region earlier in the day.

The injured passenger was flown to Wellington Regional Hospital.

A district health board spokesman said she was in a stable condition.