Instead of the rich environment depicted in the movie Finding Nemo, the coral reef will be bleached and replaced by ordinary seaweed, costing the tourism industry billion of dollars, predicts the report into the impact of global warming.
Their 350-page report on one of the world's natural wonders found no prospect of avoiding the "chilling long-term eventualities" of coral bleaching because greenhouse gases were already warming the seas as part of a process it said would take decades to stop.
"Coral cover will decrease to less than five percent on most reefs by the middle of the century under even the most favourable assumptions," the report said. "This is the only plausible conclusion if sea temperatures continue to rise."
Warmer sea waters make coral suffer thermal stress, eventually making them bleach and die.
This is because the warmer water forces out the symbiotic algae that give the coral its colour. If all are lost, the coral starves.
The Implications of climate change for Australia's Great Barrier Reef report said this could occur if temperatures increased by as little as 1º C. This is well below the 2-6º C water temperatures around the reef are expected to rise by over the next century.
"There is no evidence that corals can adapt fast enough to match even the lower projected temperature rise," it found.
Organisms that rely on coral would become rare or even face extinction, the report said.
The reef covers more than 345,000 square kilometers off Australia's northeast coast, making it the world's largest coral reef.
It consists of 2900 interlinked reefs, 900 islands and 1500 fish species; scientists consider it the world's largest living organism.
Yet the delicate habitat faces numerous environmental threats, including chemical run off from farms, over-fishing, bleaching and the parasitic Crown-of-Thorns starfish, which attacks coral.
Australia's federal government announced plans in December to reduce farm run off and ban fishing in about a third of the reef in a bid to protect Australia's number one tourist drawcard.
But the report's authors said the government needed to do more, recommending Canberra ratify the Kyoto protocol on reducing greenhouse gases and take the lead in emission reduction.
The WWF said urgent measures must be put in place to minimise reef damage and reduce greenhouse gases.
"The argument for instant action is undeniable," WWF said in a statement.
"Major reductions in greenhouse gas emissions must occur now, not in five or ten years time. This is likely to deliver major benefits to our societies both in the near-term and at times beyond 2050."