They were spade-toothed beaked whales, Mesoplodon traversii, a species previously known only from a few bones, researchers at the University of Auckland said.
"This is the first time this species -- a whale over 5 meters (16 feet) in length -- has ever been seen as a complete specimen and we were lucky enough to find two of them," Rochelle Constantine of the University of Auckland.
"Up until now, all we have known about the spade-toothed beaked whale was from three partial skulls collected from New Zealand and Chile over a 140-year period. It is remarkable that we know almost nothing about such a large mammal."
The whales were initially identified as much more common and almost identical Gray's beaked whales until a DNA analysis was done.
The researchers say they are unsure why the whales have remained so elusive.
"It may be that they are simply an offshore species that lives and dies in the deep ocean waters and only rarely wash ashore," Constantine said. "New Zealand is surrounded by massive oceans. There is a lot of marine life that remains unknown to us."
The finding was reported in the journal Current Biology.