Dr Bruce Robertson made the call after the release of a Department of Conservation (Doc) study, which he says conflicts with the conclusions made by the Ministry of Fisheries (Maf) proposing that no mortality limit be set for the squid fishery in the Auckland Islands.
"The Doc study directly contradicts Maf's assertion that by-catch of New Zealand sea lions in the squid fishery is no longer an issue contributing to the extinction of the species."
On one hand, Doc was saying the fishing effort would lead to extinction within 24 years while, on the other, Maf's fisheries model suggested the fishing effort was having a minimal impact, he said.
The Doc modelling, by its scientist Dr Louise Chilvers, who is presently on Enderby Island monitoring the population, looked at the role of disease outbreaks and fishing-related deaths during the 50% decline in the sea lion population in the past 12 years.
Published in the international science journal Polar Biology, it concluded "sustained fisheries by-catch at current estimated levels ... could result in population decline and possible functional extinction" by 2035.
It supported his research conclusions that found by-catch and resource competition with the squid fishery was causing the decline of the Auckland Island populations - not disease outbreaks, he said. It was very concerning two government departments were poles apart in their conclusions on the management of a "nationally critical" species, Dr Robertson said.
"Serious concerns have been raised about by scientists and modelers about Maf's fishery model, not the least being that it predicts sea lions will become extinct in the complete absence of squid fishing."
Maf's conclusions went against its own science advice, he said.
"We have a a level of sea lion mortality due to fishing that remains unknown at this time, which might be low or, of more concern, may be high. Clearly, it is premature to be stating fishing impacts are minimal."
New Zealand Sea Lion Trust trustee Shaun McConkey said the new evidence added to the concern the trust had about the level of advice recently given to the Minister of Fisheries by their scientists.
"They have ignored any evidence showing the squid fishery is having an impact, presented anything suggesting the impact is minimal and only given the minister one management option."
The trust believed this showed "a high degree of bias or incompetence" and considered it "unacceptable management practice" for a nationally critical species.
Maf deputy director-general resource management and programmes Scott Gallacher said the department was aware of research done by Otago University and Doc staff and would consider it in any decision making.
"Maf is confident it has access to the most up-to-date and accurate research on sea lion by-catch in the squid fishery."
Maf was analysing submissions on the position paper and would provide advice on behalf of all the interested agencies to the Minister for Primary Industries in early February, he said.
Doc spokesman Rory Newsam said Doc was concerned about the vulnerability of the New Zealand sea lion and was monitoring the population regularly.
It was working with the Ministry of Agriculture and Fisheries and the commercial fishing industry to manage threats to the species.
