Conservationists are angry at a Ministry of Fisheries proposal to remove a limit on how many sea lions can be accidentally caught by squid fishermen.
The ministry says the number of dead sea lions found in nets in the Auckland Islands is falling.
It wants to remove a limit on how many can be caught as bycatch by squid boats.
However, Otago University researcher Bruce Robertson says there is evidence from overseas that sea lions could be drowning in nets, with their bodies falling out as the nets are hauled in.
He says pup numbers on the Auckland Islands are in decline because lactating female sea lions are being killed while out feeding in the sea.
The Sealion Trust and Forest and Bird agree that fishing is affecting the Auckland Islands population.
The Deepwater Group, which represents quota owners, says fishing is not to blame for the decline in sea lion numbers.
It says resources need to be put into finding the cause of the decline.