Scientists have accused officials of hastening the extinction of the New Zealand sea lion by giving flawed advice to Primary Industries Minister David Carter.

His decision to allow more squid fishing in their sub-Antarctic territory, and to maintain the accidental kill rate, was based on ministry research that showed "exclusion" devices to prevent sea lions dying in squid nets had significantly reduced deaths.

But the advice came as scientists and conservationists presented research they say shows the $100m squid industry must be regulated to save the native species.

Otago University zoology lecturer and sea lion researcher Bruce Robertson called the decision "dangerously optimistic", and said there was no evidence exclusion devices worked, so pointing to a decline in sea lion by-catch was "deceptive and misleading”.

Sea lions have New Zealand's highest-risk classification, alongside the Maui's dolphin and kakapo. Research shows the number of pups born in their Auckland Island habitat halving since 1998.

A Conservation Department study found if sea lion by-catch continued at its current level, it could result in the species becoming "functionally extinct" by 2035. But primary industries officials called that finding "low quality" in their own advice to Carter, saying the conclusions were “not consistent with the ministry's views”.

The paper by marine mammal scientist Dr Louise Chilvers, and another by Chilvers and Robertson, failed to meet the ministry's standards, and should not be used to inform management decisions, the ministry said.

Robertson, fellow marine scientist Liz Slooten, the Greens and Forest and Bird were all outraged an internal review could override conclusions drawn by peer-reviewed research. “They're ignoring science and expert opinion,” Forest and Bird marine spokeswoman Katrina Subedar said.

Robertson said the alleged shortcomings in Chilvers' research were found not to be an issue by the journal publishing it, Polar Biology.

Primary industries deputy director-general Scott Gallacher said peer-review processes of international journals were ''highly variable''.

''The ministry scientists who rated the Chilvers and Robertson papers are highly qualified fisheries and marine scientists with 80 years' experience in scientific review.''

The ministry advice was to retain the by-catch kill rate at 68 a year, and to increase trawl tows up to a total of 4700 runs a season.

SEA LION FACTS

Total population under 10,000 and declining 1500 pups born last year – 3000 in 1998 DOC says the main barrier to breeding is trawl net deaths For every 100 squid net tows, around five sea lions are caught MPI says 82 per cent escape through "exclusion devices" No sea lions were observed dead via netting last year .

- © Fairfax NZ News