The country's population of sea lions has been on the decline for decades now but scientists say they are still getting to grips with the causes.
NIWA today said fewer than 10,000 of the mammals were left in New Zealand and the main breeding colony in Auckland had halved in size since the 1990s, putting the sea lion on the highest threat status possible.
But it's not all bad news, with small colonies on the Otago Peninsula and Stewart Island thriving while the Auckland population declines.
NIWA scientist Jim Roberts says researchers are piecing together a number of threats to sea lions to understand why the Auckland colony is doing so much worse that others.
"The comparison with Otago sea lions is telling us what these sea lions should be capable of," he said.
"It's not just pup survival or adult survival alone. Mortalities relating to interactions with trawl gear are not sufficient to explain all the changes we are seeing.
"There are a number of clues that point to nutritional stress, and disease is also affecting the number of pups who survive to adulthood."
Dr Roberts, who is assisting the Department of Conservation in creating a plan to save the mammal, said scientists were now trying to more clearly understand the prey sea lions hunted and how its availability was changing in Auckland.
"I feel we are beginning to solve some aspects of this puzzle. It looks very much like the sea lions are suffering nutritional stress as a result of changes in prey availability around the Auckland Islands, and some years it might be quite extreme," he said.
They were also trying to better understand the causes of disease epidemics in the animal's population to prevent more outbreaks, he said.