It seems a dispute over the commercial shark fishery off the coast of southern Australia has failed to be resolved, despite two court cases, a review and a change to how allocations are managed.

The Southern Shark Fishery includes waters off Tasmania and Victoria through to the Great Australian Bight, and provides more than 2,000 tons of the shark commonly used in fish and chips.

The Australian Fisheries Management Authority (AFMA) has announced a new management programme for the fishery, which will see some fishers gain quota while others will loose.

But Chair of AFMA Wendy Craik says she's not expecting smooth sailing from here on in. "One of the real difficulties when you have an issue of reallocation is that the total size of the pie remains the same and if you're allocating something in a different way from the way it was initially allocated then clearly there will be some people who are winners and some who are losers.

"I think some people will be pleased that they are getting a greater allocation that they had and others will not be pleased that the allocation they had they no longer had and I suspect we will see well I'd be surprised if we didn't see some appeals."