Conservation Minister Nick Smith has called for fishing vessels around Campbell Island to use devices that repel sea lions, after 16 were killed in the first three weeks of the season.
But the Government doesn't have any regulatory capacity to enforce their use and the Green Party is calling for the fishery to be closed altogether.
Dr Smith says the number of sea lions drowning is unacceptable and he hopes the exclusion devices will put a stop to the deaths.
"The sea lion is attracted to the fish and wants to get a cheap easy feed. He dives down into the net and effectively get crushed and drowned within the net. This device effectively flips the sea lion out of the net before he gets trapped and drowned."
Greens co-leader Metiria Turei says there isn't enough evidence to show the exclusion devices actually work and the fishery should be closed until their effectiveness is proven.
She says 16 deaths in three weeks is a significant number.
The total population of the New Zealand sea lion, formerly known as the Hooker's sea lion, is estimated at between 10,000 and 12,000, with 20% breeding on Campbell Island. The remainder breed on three of the Auckland Islands and a few on the Otago Peninsula.