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As only four pups were born during the last breeding season, the Otago population failed to grow and might have declined, he said.
"It's unusual to find one but to find four ... the mysterious deaths are certainly cause for concern."
It was not just an Otago problem as the latest figures on the Auckland Island population showed the third-lowest pup production ever reported.
Department of Conservation scientist Dr Louise Chilvers said the pup production estimate for the Auckland Island population for 2011-12 was about 1683.
In the late 1990s the population was estimated at 3021 but had steadily declined to a low of 1501 in 2008-09.
"They are still nationally critical and that's where they'll be staying."
The slight increase from the previous year's 1550 was within the natural fluctuations expected from year to year.
"Half the beach is still empty relative to where it was 12 years ago," she said of the Auckland Island beaches on which pups were counted.
Mr McConkey said the concern was the fishing industry and Fisheries Ministry would use the slight increase as justification for continuing to lessen limits on sea lion by-catch.
"It does not indicate everything is fine and they're doing well.
You can't say ... they're no longer in danger."
They were continuing to lobby the Government for more communication about its management strategies but with little success, he said.
In Otago, the population had a bad year with four sea-lion deaths, including two females, whose cause of death was not clear. Of the two males, one was shot and the other died of a bacterial infection.
While a few years ago it was normal to see 50 sea lions on Otago beaches, now it closer to 30 to 40 on the main beaches, he said. There were also tagged sea lions which had not been seen for a few seasons.
Bacterial infections had hit the Auckland Islands hard in the past but had not affected the Otago population, possibly because they were healthier and well-fed.
"We need to get a better handle on if those who have disappeared have died or are just hiding out of sight."
Dr Chilvers said there were still a lot of things they needed to understand about sea lions, such as why they were low reproducers compared to other sea lion species.
There was also the impact of environmental change and resource competition.