It's understood police have identified the man.
Wellington Mayor Celia Wade-Brown said on Twitter that it would be a "sad Christmas for [the diver's] friends and family".
Details about what happened were "still sparse", police said.
Despite the inclement weather, sea conditions in the area were said to be calm.
The diver was found in an isolated and rugged stretch of Wellington's south coast, accessible only by 4WD or by walking for about 45 minutes from a marine education centre.
Red Rocks/Pariwhero is a scientific reserve located between Owhiro Bay and Sinclair Head, on Wellington's south coast.
The unusual rock formation has a popular walking and cycling track from Owhiro Bay Quarry, and a four-wheel drive track.
It is close to the end point of the Taputeranga Marine Reserve, where fishing and hunting is banned, which makes it a popular spot for diving, according to the website New Zealand Unwrapped.