Although the reef is one of the world's most protected marine environments, its coral cover has declined from 28 percent to 13.8 percent in the past 27 years, with two-thirds of the decline occurring since 1998, researchers from the Australian Institute of Marine Science reported.
The scientists writing in the Proceedings of the National Academy of Sciences said storm damage was responsible for 48 percent of the decline while crown-of-thorns starfish -- voracious consumers of coral -- contributed 42 percent.
Coral bleaching caused by rising water temperatures accounted for another 10 percent of coral loss.
"We are basically losing an ecosystem that is so iconic for Australia and the rest of the world," institute scientist Katharina E. Fabricius told The Washington Post.
The study findings will be "a shock to the system" that could force Australians to focus on the issue, a U.S. researcher said.
"If anyone's going to do it, it's going to be the Australians, because they really care about the Great Barrier Reef," Nancy Knowlton, a coral reef biologist at the Smithsonian Institution National Museum of Natural History, said.
At the current rate of coral cover decline, researchers said, the Great Barrier Reef would lose half of its remaining coral cover by 2022.
"It will be really very low in 10 to 15 years," Fabricius said.