A review of the scientific research on the sea lions by University of Otago zoology senior lecturer Dr Bruce Robertson investigated nine possible causes of why the subantarctic Auckland Islands population was experiencing a decline in sea lion pups but on the only other breeding spot for the mammals, Campbell Island, numbers were slowly increasing.
Between 1998 and 2009, the Auckland Islands' pup population dropped 40% from 3021 to 1501.
Dr Robertson, whose research has been published in the journal Mammal Review, said the intention was not to apportion blame but when the information was objectively reviewed, possible causes such as natural predation, disease, pollution and environmental change were ruled out.
The main difference between the two populations was the squid fishery, he said. At Campbell Island, the fishery was not operating close enough to cause a problem for the breeding colony.
However, on the Auckland Islands most sea lions caught in fishing nets were female and there was a direct overlap between breeding females' feeding sites and the fishery.
Sea lions did not go far from their pups and the squid was abundant and "right on their doorstep".
"There is definitely resource-based competition. [The fishery] is taking away a resource the sea lions need and rely on."
That competition would put female sea lions under stress and reduce their reproductive ability.
He hoped the review showed where research needed to be targeted.
Ministry of Fisheries deep-water fisheries manager Aoife Martin said while there was no evidence to suggest there was resource competition between sea lions and the fishing sector, research was under way to investigate it.
A mortality limit restricting the amount of fishing activity in that area was set every year based on a comprehensive sea lion population mode developed by the National Institute of Water and Atmospheric Research, she said.
"It is apparent that the sea lion population has declined, although there is no information to suggest that this is due to fishing activity. The ministry can confirm that the actual number of reported captures of sea lions is declining, with zero captures reported in this year's squid fishery which recently ended."
All squid fishing vessels in the southern squid fishery had sea lion exclusion devices fitted to their fishing nets, Ms Martin said. These devices allowed any sea lion that had accidentally entered into the fishing net to escape.