New Zealand Sea Lion Trust co-chairman Shaun McConkey said until the cause of the sharp decline was understood, there should be a ban on fishing where sea lions foraged in the area.
The dramatic drop in the number of sea lion pups — 24% below last year’s count — indicated the squid fishery management strategy in place for the past four years was not working.
"The Auckland Island pup count in 2023 was the lowest on record since annual reporting started in 1995.
"The fishery can have direct effects on sea lions, such as deaths from fishing gear interactions, and indirect effects on sea lions, such as reducing the available food in the sea lions’ foraging grounds around Auckland Island [Motu Maha].
"These indirect effects can occur through catching of sea lion prey species, and damage of the marine habitat, and through fishing techniques such as bottom trawling."
In the trust submission to the recently closed consultation on the southern squid trawl fishery operational plan, Mr McConkey said the trust had "grave reservations" that none of the options under consideration would minimise the effects on the marine mammals.
Forest & Bird Otago Southland regional conservation manager Chelsea McGaw said the organisation held similar concerns.
The low pup count this year represented a "massive decline" in what was a "stronghold" for the species.
"Only 1.5% of the population is on the mainland coast and it isn’t even big enough to be considered a breeding colony yet, so the Auckland Island population is incredibly important," she said.
Fisheries New Zealand acting director fisheries management Robert Gear said the reason for the decline was unclear and was being investigated by the Department of Conservation (Doc).
"It cannot be linked to a disease outbreak and there has been no associated increase in sea lions being caught by fishing vessels."
The organisation said the 2019-23 plan was due to expire at the end of next month, but the low pup count had triggered a review.
Monitoring this year produced an estimated pup count of 1278, "a marked decrease in numbers" after pup counts averaged 1730 pups a year over the past decade, consultation documents said.
Commercial fishing was banned within 12 nautical miles of the Auckland Islands after the area was designated a marine reserve in 2003, but sea lions foraged beyond the limit and there was overlap, it said.
The proposal was to keep the management approach similar to the present four-year plan, but to put a greater emphasis on female sea lion captures because of their significance to reproduction.
The present annual fishing-related mortality limit of 52 sea lions was proposed to be reduced to either 24 sea lions (or 12 female) or 48 sea lions (24 female).
Minimum observer coverage of the southern squid trawl fishery would decrease to a proposed 50% or 70%.
The new management plan would be reviewed in five or 10 years, it said.
Mr McConkey said the New Zealand Sea Lion Trust welcomed Doc’s investigation into possible causes of the low pup count, including "changes in female sea lion breeding rates, food availability, climate change and disease".
However, until Doc made recommendations based on findings, a precautionary approach towards sea lions was required.