The death, in the fishery near the sub-antarctic Auckland Islands, was recorded in a Ministry for Primary Industries weekly monitoring report.
It happened just seven weeks into the fishing season.
The report said the female sea lion was found beside an exclusion device in the net that was meant to allow sea lions to escape.
Forest and Bird spokesperson Kevin Hackwell said there was no evidence to show the exclusion devices actually worked.
"It is a critically endangered population and we don't think that the present methods that are used to try and avoid deaths in the trawl fishery for squid are adequate to protect the sea lions."
The government should place a moratorium on trawling in the area next to the Auckland Island marine mammal sanctuary until there was evidence showing the exclusion devices worked, Mr Hackwell said.