For the past 30 years, this was done by counting the penguins from photographs. But in the past three years, specially developed semi-automated software has sped up the process immensely.
A helicopter platform was used to photograph colonies on Ross Island, and on Beauford Island when sea ice extended that far. A C-130 Hercules was needed to reach colonies spread out over 1000km further up the Victoria Land coast.
More recently, satellite imagery has been used to conduct an Antarctic-wide census of Adelie penguins, said Landcare Research ecologist Phil Lyver.
The technology had also been used to discover Adelie penguin colonies for the first time.
Dr Neil Gilbert, Antarctica New Zealand's environment manager, said keeping long-term datasets could allow scientists to track fluctuations in food source and habitats, or changing temperatures.
"Obviously, penguins are an iconic species when you think about Antarctica, and we want to make sure we understand the populations, because of the value they have in Antarctica, and because our management of Antarctica depends what's going on there," he said.
"The other reason is they are indicators of climate change and we want to understand how Antarctica is going to change, and what the effect of that is going to be on New Zealand and the rest of the world."