AFMA has developed protected species management strategies and commercial fish species rebuilding strategies where concerns have been identified about the impact of commercial fishing on their sustainability.

AFMA has developed protected species management strategies for Australian sea lions, dolphins and upper slope dogfish which outline management arrangements to minimise the impact of fishing on these species. The strategies involve unique management arrangements tailored to reducing interactions with each species. Arrangements can include things such as area closures, gear restrictions, monitoring requirements or trigger limits.

Commonwealth longline fisheries are also covered by the Seabird threat abatement plan.

For overfished stocks, AFMA must cease targeted fishing and develop a rebuilding strategy to rebuild the stock to above its limit reference point, for agreement by the fisheries and environment Ministers as relevant. A rebuilding strategy will be required until the stock is above the limit reference point with a reasonable level of certainty. Adequate monitoring and data collection must be in place to assess the status of the stock and rebuilding progress and satisfy requirements of the Environment Protection and Biodiversity Conservation Act 1999.

Incidental mortality on overfished stocks should be constrained as much as possible to levels that allow rebuilding to above the limit reference point within the specified timeframe.

A rebuilding strategy must include performance measures and detail on how and when these measures will be reported on. Where there is no evidence that a stock is rebuilding or is going to rebuild in the required timeframe, AFMA will review the rebuilding strategy and make the result of the review public. If changes to the rebuilding strategy are considered necessary, such changes must be made in a timely manner

Current rebuilding strategies: