It was identified by its distinctive dorsal fin as being the famous Migaloo -- a whale that usually migrates past Australia.
Another special sighting was a newborn humpback calf on July 7, only the second reported in New Zealand.
Blue and sperm whales and a southern right whale were also seen by the survey team.
The DoC research, in partnership with OMV New Zealand, aims to estimate size of the New Zealand humpback whale population and assess humpback whale recovery since commercial whaling ceased in 1964.
The annual surveys are timed for humpback whales' northern migration from Antarctica to warmer South Pacific breeding grounds.
"The higher number of humpback whales being seen indicates the New Zealand population is recovering but we are not yet seeing the extraordinary rates of increase they have in Australia of around 11 per cent a year," survey leader Nadine Bott said.
"Perhaps that is something we will enjoy in our waters in the future."
The survey is carried out with the help of volunteers including six former whalers who lead the whale spotting from a high point on Arapawa Island overlooking Cook Strait.
Whales seen are approached by boat to collect photos and skin samples using a biopsy dart tool that is used to identify individual whales.
"The ex-whalers are highly experienced and committed and have been invaluable to the project, especially our success in observing so many whales," said Ms Bott.
Humpback whale recovery will be assessed by comparing numbers seen in the surveys to whalers' records of humpbacks in Cook Strait from the 1950s and early 1960s.
Humpback whales' inquisitive nature, large flippers and tail, and their propensity to roll makes them particularly vulnerable to getting caught in craypot lines as they migrate along the New Zealand coast.
Two humpback whales were seen in separate encounters this year with craypot line caught on them and line and buoys trailing behind.
The two entangled whales were moving too fast for a specially-trained DoC whale disentanglement team to have time to get to them and try to cut the line off them.
DoC says that people setting craypots can reduce the risk of whales getting entangled in them by minimising floating slack craypot line, allowing only enough for tidal action, and avoiding setting pots during June and July in offshore deeper water.