One of the most mysterious whales of the ocean has been spotted off the Northland coastline, marking the first time it has ever been seen alive in New Zealand waters.

Project Jonah today announced the exciting and rare sighting of three Gingko toothed beaked whales swimming offshore at the top of the North Island in January.

To date most information about the elusive whales that live in the deepest depths of the planet has been gleaned from beach strandings, with some species never seen or photographed alive.

The once-in-a-lifetime encounter happened during a survey of marine life by the Far Out Ocean Research Collective at the Parengarenga Canyons approximately 10km east of North Cape.

A pod of three mysterious Gingko-toothed beaked whales were seen for the first time swimming in the Southern Hemisphere. Photo / Facebook

The group, on its sixth day of sea survey, had already come across a Bryde's whale before spotting another whale blow, which they changed course to investigate. This turned out to be a small group of three beaked whales, marking the first confirmed live sighting at sea of this species in New Zealand.

The collective posted a series of captivating photos of the trio swimming in the inky blue ocean, snapping the crucial beak photo, and showing one blowing as it surfaced to breathe. The photos were sent to two top whale experts for identification.

"This is incredibly exciting. As far we know, there are no confirmed live sightings at sea of this species in New Zealand, only a handful of stranding records," posted the collective on their Facebook page.

"Beaked whales are mysterious creatures, due to their shyness of boats, offshore range and deep-diving habits, spending long periods of time underwater.

"Most of what we know about them is from beach strandings, and some species are hardly ever seen or photographed alive.

"We were lucky to snap a few photos, including of the beak of one of them, which helps to identify the species.

"As far we know, there are no confirmed live sightings at sea of this species in New Zealand, only a handful of stranding records.

Because so little was known about the creatures of the deep the collective sent photos to Anton van Helden and Wojtek Bachara for expert confirmation.

They suggested the mammals were the rare Gingko-toothed beaked whales.

Project Jonah said it was a very exciting day, making this the first confirmed at-sea sighting for the species in New Zealand and possibly the Southern Hemisphere.