The fishers target gummy sharks, which are sold as flake in fish and chip shops, but their nets occasionally trap sea lions and dolphins, reports ABCNews.
A ban on gillnet fishing in areas mainly along South Australia's west coast and Eyre Peninsula was extended last October for 18 months to protect sea lions from nets and to gain more data during their breeding cycles.
However, Kyri Toumazis from the Shark and Gillnet Fishermen's Association says without fishers and their boats in those waters, there is little monitoring of the endangered species.
"Really there hasn't been any investment from the conservation perspective to actually do any more work on the sea lion numbers to see if those closures are actually warranted," he said.
He says the local industry is struggling to absorb the closures.
"Some have chosen to relocate their businesses in Bass Strait and I'm aware of three vessels that left South Australia," he said.
The Australian Fisheries Management Authority says no sea lions have died since the latest closure but the overall gillnet catch has also decreased.
It says it continues to work with the industry and conservationists over the issue and the use of hooks to catch gummy sharks is being investigated.
