The reef, which stretches for 1,200 miles off the northeast coast of Australia, has "poor" prospects of survival as a result of over-development and a failure by the relevant authorities to protect it from illegal fishing and chemical run-off, the Great Barrier Reef Marine Park Authority said its first report on the state of the reef's health.
The report warned that damage to mangroves, increasing algae on coral reefs, ocean acidification and coral bleaching were already evident.
"While populations of almost all marine species are intact and there are no records of extinctions, some ecologically important species, such as dugongs, marine turtles, seabirds, black teatfish and some sharks, have declined significantly," it said.
"Disease in corals and pest outbreaks of crown-of-thorns starfish and cyanobacteria appear to be becoming more frequent and more serious."
The Outlook Report 2009, found climate change, declining water quality from coastal runoff, development and illegal fishing were the biggest dangers to the reef.
While the World Heritage-protected site, which sprawls for more than 133,000sq miles and is the world's largest living organism, is in a better position than most other reefs globally, the risk of its destruction was mounting.
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"Even with the recent management initiatives to improve resilience, the overall outlook for the Great Barrier Reef is poor and catastrophic damage to the ecosystem may not be averted," the report found.
"If changes in the world's climate become too severe, no management actions will be able to climate-proof" its ecosystem, it said.
The study echoed findings by scientists belonging to the UN Intergovernmental Panel on Climate Change that the Great Barrier Reef could be "functionally extinct" within decades, with deadly coral bleaching likely to be an annual occurrence by 2030.
Improving water quality and further research into the effects of fishing were among initiatives that will give the reef the best chance of adapting to the "serious threats" ahead, the authority said.
The Australian government responded to the report with a plan to cut the amount of pollution reaching the reef in runoff water from agricultural land.
The reef, which is larger than Italy, contributes about $A5.4 billion to the Australian economy through tourism, fishing and other industries and supports more than 50,000 jobs, according government figures.