The industry says the new plan would cripple the R5.5 billion pelagic fishing sector.
The matter has been set down for hearing in the Pretoria division of the Gauteng High Court in October.
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Implementing proposals by conservationists for revised "no-take" fishing zones around African Penguin breeding islands would cost the pelagic fishing industry as much as R190 million a year, the South African Pelagic Fishing Industry Association says.
Under the current no-take zones, the industry is forfeiting R90 million a year. These closures were introduced around six islands in October last year to help slow the slide in penguin populations and confirmed in July this year by former environment minister Barbara Creecy.