A rare female sea lion has been found dead - presumed drowned - in the trawl net of a squid fishing boat.

The net was fitted with a specially designed escape hatch but it appears not to have worked. The Ministry for Primary Industries said far fewer sea lions have died in trawl nets since the escape hatches were introduced, and this was the first observed sea lion death, seven weeks into the season.

But Forest & Bird said the death of the sea lion was unacceptable and showed squid fishing trawlers could not guarantee the safety of the rare species or prove the escape hatches worked.

The sea lion was found by an official observer in the net of a boat trawling at the squid fishery at Auckland Islands about two weeks ago. The animal was reportedly found uninjured and pressed against the hatch, suggesting it had been unable to escape and had drowned.

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"New Zealand sea lions are critically endangered and without urgent action to reduce threats to their population, especially breeding females, we may be the last generation to coexist with this species," Forest & Bird marine advocate Katrina Goddard said.

"If the Ministry of Primary Industries and the Department of Conservation are serious about saving this unique species, they should stop sheltering the fishing industry from having to prove Sleds [sea lion exclusion devices] work, and put a moratorium on trawling in the area next to the Auckland Island marine mammal sanctuary until that research is available."

Since Sleds were introduced the number of sea lions killed has fallen from an estimated 20 to 30 per year to between one and four per year since 2010, according to MPI.

Studies showed around four out of five sea lions that enter trawl nets fitted with Sleds would escape, MPI said. "This unfortunately means that sea lions will occasionally be captured in trawl nets."

As of March 19 there had been 661 tows in the fishery, of which two-thirds were observed. Among those, this was the first sea lion to be killed, MPI said. Last year no sea lions were observed to be captured, and only one in 2015.