The team, who regularly head out on the harbour as part of a joint satellite tagging programme, observed eight in one spot on January 17.
"It was by far the largest number of white sharks we've ever seen in the Kaipara Harbour in a single day," Mr Duffy said.
After tagging one of the sharks, another 3m great white was discovered swimming around a float where their boat was anchored.
Mr Duffy said some nearby fishermen also caught one of the sharks, but broke it off the line as soon as they realised what they had caught.
A further three were found at the same site the next day, but none have been seen there since.
It was unclear why so many have been spotted together at once.
"We speculate that they were feeding on fish coming off the tidal flats as the tide fell, but then the next day, when we saw similar conditions, we didn't see any more."
The encounter comes after a spate of great white sightings this summer.
Last month, a 4.5m shark was spotted in the Waitemata Harbour, while a family holidaying at Leigh reported one "the size of a tractor" leaping from the water.
The mass sighting was important because little is understood about the distribution and population of great whites in New Zealand, which is considered a "global hot spot" for the protected species.
Information gathered from previous captures and sightings suggested the upper North Island was an important breeding area for the species, and potentially also a nursery area for juveniles, Mr Duffy said.
"The missing piece of the puzzle is where are the juveniles coming from - the sharks appear to be breeding in New Zealand, so do we have our own breeding population, and if so, are there identifiable nursery areas?"
The link between great whites and harbours, such as the vast Kaipara, also remained a mystery.
"We know they are quite regularly seen in harbours, but we don't know how much time individual sharks spend in them."
Many boaties had sent Mr Duffy images of what they wrongly assumed were makos in harbours.
"There is a reluctance among people to think they've seen a great white shark," he said.
International satellite tagging programmes have transformed our understanding of great whites, proving the species didn't just stick to coastal zones in temperate waters, but made annual migrations across open ocean to the tropics.
However, none had yet been observed travelling from Stewart Island - a major congregation point for larger sharks - to the upper North Island.
This was despite sharks tagged in the upper North Island journeying to Queensland, and a shark tagged in South Australia later turning up in Ahipara in Northland.
Female great whites around the lower South Island tended to disappear when they matured and became pregnant, "but we don't really know where they go".
