A 100-strong team from the ARC Centre of Excellence for coral Reef Studies, at James Cook University in Queensland, has been mapping the area for months using aerial and underwater surveys.
The scientists say their findings point to climate change as one of the causes behind the coral bleaching.
The center director Terry Hughes said: "This year is the third time in 18 years that the Great Barrier Reef has experienced mass bleaching due to global warming, and the current event is much more extreme than we've measured before."
There has been a 35% average death toll for the coral reefs at the World Heritage site that stretch for 2,300km (1,429 miles), according to the survey.
Coral bleaching takes place when sea temperatures rise, even by as little as one degree Celsius, say the researchers. At that point, the tiny algae living in the corals, called zooxanthellae, are expelled. With their primary supply of energy gone, the coral then turns white, hence the "bleaching."
The team surveyed 84 reefs alongside the north and central sections of the Great Barrier Reef, with severe discrepancies found between the two.
According to the study, the north side is far more affected, with death toll rates between 50-60%, and bleaching rates close to 90% in some areas.
Southward of Cairns, Queensland, on the central Great Barrier Reef, the "average mortality is estimated at only 5%," with 25% bleaching rates, the scientists report.
Bleached coral doesn't die immediately -- in fact, if the water temperature goes back to normal levels, in a couple of months, the algae can return to recolonize the coral and preserve the reef. If water temperatures don't decrease, the coral can die.
Once that happens, the space is taken over by seaweed, which grows quickly and prevents coral from growing back, the scientists explained.
'Rainforests of the sea'
John Pandolfi, one of the project coordinators at the center for reef studies, told CNN that the reasons behind coral bleaching are "the El Niño year, the very high, anomalous sea temperatures, along with very low cloud cover."
In the north part of the Great Barrier Reef, which has been the most affected, this means that "it's very, very hot and very, very sunny," he said. By contrast, corals in the central region of the Great Barrier Reef had a stroke of luck in the form of a "serendipitous Fiji cyclone which cooled the water down" with high rainfall.
Coral bleaching might sound insignificant compared to elephant poaching or deforestation, which are much-publicized environmental problems, but Pandolfi says coral reefs "provide an enormous amount of services -- food, economical security, natural harbors; over 100 countries rely on coral reefs for subsistence fishing or tourism."
In addition, Pandolfi points out that "even though coral reefs only make up 0.25% of the area of the world's oceans, they comprise 25% of its biodiversity. They are the rainforests of the sea." The Great Barrier Reef in particular, "in sheer amount of reef area, is truly the greatest on the planet."
Without the reef, Australia would likely lose a $6 billion tourism industry, alongside endangering food security in the coastal region, Pandolfi said. "Would tourists want to go look at dead reefs?" he wondered.
"Global gas emissions need to be brought down under control" in order for the bleaching to cease, Pandolfi told CNN.
But climate change isn't the only cause behind the phenomenon. Coral reefs tend to get "stressed" by different elements which slow down their growth and make it harder for bleached coral to regenerate, he explained.
Some of these stresses are man-made, such as farming pollutants, fertilizers and pesticides which get dumped into the sea. Over-fishing, erosion and coastal development also play a part, he said.
"If we can keep the non-climate stressors to a minimum, the reefs will be in much better condition to cope with future global warming," said Pandolfi. "We have to treat ocean and land as an integrated unit."
Australia is the latest country to declare a coral bleaching crisis. Thailand recently closed down diving sites due to the same phenomenon.