"It could be a very dangerous decision," Dr Bruce Robertson, of the University of Otago, said.
The Government this month backed down on a proposal to drop the sea lion mortality limit in the Auckland Island squid fishery, instead leaving the maximum number of deaths for the 2012-13 season at last season's total of 68.
"The increased certainty of information now available about sea lion exclusion devices means we can be more precise about the management of the fishery."
The decision would be reviewed in four years or sooner if it was shown fishing was affecting sea lions.
A discount for using the device meant vessels could carry out more trawl tows, up to a total of 4700 per season.
Dr Robertson, a senior lecturer in the department of zoology, said it was a dangerously optimistic decision given there was no evidence dead sea lions were retained in trawl nets by the devices and therefore seen and counted.
"The decline in bycatch could be just as likely explained by changes to [the devices] now unintentionally allowing dead sea lions to be ejected from nets and hence not recorded."
He questioned the science and modelling behind the Government's decisions, as there had been no experiments or research on whether the changes to the devices were effective.
"Based on previous modelled catch rates, there could be over 250 sea lions killed if 4700 tows are undertaken in the fishery."
He acknowledged the Government had accepted some of the advice given through the discussion paper process by agreeing to review some of the modelling on which it based its sea lion mortality counts.
Green Party ocean spokesman Gareth Hughes said the minister should endorse the sea lion-friendly fishing method of jigging, rather than the "lethal" trawling method.
"We don't allow game hunters to accidentally kill kakapo or great spotted kiwi. We shouldn't allow the squid fishery to kill any of our critically endangered New Zealand sea lions."
Forest and Bird said the minister had "dropped the ball" on the issue, as research showed the sea lion population would continue to spiral downwards towards extinction unless steps were taken to reduce the effects of fishing.
New Zealand Seafood Industry deepwater group chief executive George Clement said the minister's decision recognised squid fishing was not to blame for a decline in sea lion pups, and the reason behind the decline needed to be found.
"Our industry has gone to great lengths to ensure fishing does not harm the sea lions. We have refined sea lion exclusion devices. This had been a major achievement."
