The controversial death of a female New Zealand sea lion has sparked outrage among environmental and conservation organisations Forest & Bird and WWF New Zealand.

The New Zealand sea lion, a critically endangered species, drowned in a squid trawl net in the Auckland Islands, resulting in pleas to change the method of catching squid within the fishing industry.

Forest & Bird oceans advocate Anton van Helden was saddened by the death of the animal, highlighting that the New Zealand sea lion is the world's rarest species of sea lion.

"With less than 12,000 animals remaining, each life is important," van Helden said.

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"In fact the loss of a female is particularly hard as she may have a nursing pup ashore, and be pregnant with next year's pup; a loss of three animals in one hit."

Van Helden was unsatisfied with the fishing industry's attempt to implement Sea Lion Exclusion Devices (SLEDs), which were intended to remove observable by-catch.

"There is no evidence to show SLEDs don't just eject dead and injured animals, preventing them from being accounted for by official observers," van Helden said.

"We have no way of knowing the actual number of sea lions that pass through the SLEDs."

Instead, van Helden sought the introduction of jigging, a sea lion-friendly fishing method.

"Industry arguments about it being not economic and unsafe are anecdotal, and are at odds with research that shows jigging fisheries operate in similar sea conditions in other parts of the Southern Ocean.

"We need to take a precautionary approach to save our only endemic sea lion."

Van Helden's propositions were echoed by Worldwide Fund for Nature (WWF)-New Zealand chief executive Livia Esterhazy, who wanted the removal of fishing nets in New Zealand.

"We understand that accidents happen, but for New Zealand sea lions to recover, we need the Government to work to reduce the number of sea lions accidentally killed in fishing nets to something very close to zero," said Esterhazy.

"Fishing nets are the biggest human-made threat to these precious animals, so it's important that we take a precautionary approach to fishing in their habitat.

"This particular NZ sea lion was found dead up against a SLED, something intended to let sea lions escape from fishing nets. This shows that these devices don't always work.

"For years, we've been calling for the government to carry out research to determine how often and how well these devices actually let sea lions escape from fishing nets alive. Now, 2018 is the year to get this research done."