Rescuers and volunteers worked all day on Saturday to refloat about 25 of the animals, part of a pod of about 40 to 50 pilot whales who got stranded earlier that day on a beach in the Coromandel Peninsula.
Despite efforts to bring them out to sea, five dead pilot whales were discovered late on Saturday night at a site thought to be the original stranding location, the department said.
"Although the high tide at about 9 p.m. on Saturday night had allowed the stranded whales to be refloated, members of the pod restranded this morning - including several on rocky outcrops at the bay," the Department said in a statement on its Facebook account.
"Sadly, about dozen have died after restranding on the rocks this morning. However, we are encouraged by the fact the majority of the stranded whales have re-joined the pod this morning and have been chaperoned out to deep water."