The dire warning from the government-funded agency is at odds with the official line from Australian Prime Minister Tony Abbott, who in 2009 declared the science of climate change was "crap".
Abbott last year scrapped a tax on carbon pricing and abolished the independent Climate Commission, saying recent severe droughts that have crippled cattle farmers were "not a new thing in Australia."
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As the host of the Group of 20 last year, he attempted to keep climate change off the agenda, resulting in an embarrassing backdown at the Leaders Summit in Brisbane after U.S. President Barack Obama used a high-profile speech to warn Australia that its own Great Barrier Reef was in danger.
One of the world's biggest carbon emitters per capita, Australia has declined to join the United States, Japan, France and others in contributing to the United Nations' Green Climate Fund.
Abbott has instead committed A$2.55 billion ($2.21 billion) to a domestic initiative to reduce the country's emissions by 5 percent below 2000 levels by 2020.
The new research by CSIRO and the Bureau of Meteorology, using some 40 global climate models, has Australia warming at a greater rate than the rest of the world.
The 5.1 degree celsius projection for 2090 is at the top end of a range starting at 2.8 degrees celsius and is dependent on how deeply, if at all, greenhouse gas emissions are cut. The world average is for an increase of between 2.6 degrees celsius and 4.8 degrees celsius.
The report said the annual average temperature in Australia would likely be up to 1.3 degrees celsius warmer in 2030 than the average experienced between 1986 and 2005.