A new colony at Tawhitinui Bay, a fairly sheltered part of Te Hoiere/Pelorus Sound, actually gained about 22 birds in the last three years.
A vulnerable rare bird species has lost a quarter of its population in three years, prompting a slew of theories and calls for reclassification.
A second aerial king shag census has recorded a large drop in the number of birds in the Marlborough Sounds, down to 634, which is about 200 fewer than the first census in 2015.
The drastic drop in just three years has residents, industry bosses and conservationists worried about whether aquaculture, climate change or other causes are to blame.
Ornithologist Rob Schuckard said in his report on the census most of the 12 breeding colonies, which are only found in the Marlborough Sounds, had shrunk by an average of 24 per cent.
The largest colony at Duffers Reef, in the outer Te Hoiere/Pelorus Sound had lost about 85 birds, he revealed in the report.
However the Tawhitinui colony, also in Te Hoiere/Pelorus Sound gained about 22 birds, while the Ruakaka-Blackwood colony in the Queen Charlotte Sound gained five, calculated using averages numbers from three different assessors.
The new results were at odds with expert advice given at aquaculture resource consent hearings in previous years about the stability of the population, despite increasing industry in the Sounds.
The census was commissioned by New Zealand King Salmon (NZKS), which agreed to check the population every three years as part of resource consent conditions for its Waitata and Kopua salmon farms.