The report also says changes in ocean currents and rainfall could affect fish and shellfish numbers, says ABC News.
Queensland Seafood Industry Association says the management of the fishing industry must become more flexible.
The association's Robin Hansen says the industry is taking the report seriously, but it needs to know more about time frames.
"I don't think we'll be taking these sort of concerns lightly, but it's not something that we are really sure about how quickly, how soon and how much and I think those are the sorts of things that we will factor into any sort of management changes that are likely to be made into the future," he told ABC.
Mr Hansen says flexibility is the key to a successful, sustainable future in the fishing industry.
However, much of Tasmania's fishing industry says that the report is no cause for panic.
The report predicts salmon, abalone and rock lobster in southern fisheries will be affected by rising water temperatures over the next 50 years.
According to ABC it says climate change will have significant impacts on biological, economic and social aspects of the Australian fishery.
But Tasmania's fishing industry say it is too early to be alarmed.
Tasmanian Aquaculture and Fisheries Institute director, Colin Buxton, says there are options like selectively breeding fish tolerant of higher temperatures.
"We know that this is happening but I don't think there's any cause to panic at the moment," Mr Buxton told ABC.
Meanwhile, the South Australian rock lobster industry could be one of the commercial fishing areas affected most by climate change in Australia.
The Federal Government's preliminary assessment of the effects of climate change on the aquaculture industry calls for the implementation of strategies to ensure the long-term survival of fisheries and aquaculture businesses.
The report shows that a large stretch of the south-east coast will feel the largest effects of rising water temperatures, acidity, salinity and sea levels.
It indicates that the numbers of ground dwelling fish stock such as crayfish will be highly affected by these factors, reports ABC.
In contrast, federation president Dr Trevor Anderson is confident the prawn industry will not be affected because it already copes with varied conditions.
He told ABC: "Most of the aquaculturists that I know are very innovative people, in fact it's an industry that's characterised by innovation, so I don't see anybody in the aquaculture industry suffering too badly unless there are huge changes and then we really can't predict what the outcome will be,"
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