Primary Industries says proposed snapper spawning closures in Spencer Gulf and Saint Vincent Gulfs may not be permanent.
The department has proposed closing areas to fishing for several months from November, due to stock depletion.
Some councils say several towns would be likely lose a significant part of their summer tourism trade as a result.
Department executive director of aquaculture and fisheries, Professor Mehdi Doroudi, said annual assessments of fish stocks would continue.
"We are just proposing to close some key areas because we need to give this protection to snapper," he said.
"We want to put these measures on an annual basis, rather than make them permanent closures [and] subject them to further reviews.
"When the stock starts bouncing back then you can lift these measures."