The 2,300 kilometre World Heritage Site suffered its most severe bleaching on record last year due to warming ocean temperatures during March and April.
"We are very concerned about what this means for the Great Barrier Reef itself and what it means for the communities and industries that depend on it," said Russell Reichelt, Chairman Great Barrier Reef Marine Park Authority in Australia.
"The amount of coral that died from bleaching in 2016 is up from our original estimates and, at this stage, although reports are still being finalised, it is expected we will also see an overall further coral cover decline by the end of 2017," said Reichelt.
It is now confirmed an estimated 29 per cent of shallow water corals died from bleaching in 2016. Coral bleaching did extend to deeper corals beyond depths divers typically survey to, but mortality cannot be systematically assessed.
This is up from the original estimated 22 per cent in mid-2016, with most mortality occurring in the north of the Reef, researchers said.
The most severe mortality was confined to the area north of Port Douglas, where an estimated 70 per cent of shallow water corals died and there was significant variability between and within reefs.
This is in addition to ongoing impacts from crown-of- thorns starfish, coral disease and poor water quality from coastal run-off.
The 2017 pattern of bleaching was similar to 2016, but most severe in the centre of the Reef between Cairns and Townsville. Ongoing thermal stress is also causing elevated coral disease.
Tropical cyclone Debbie impacted around a quarter of the Reef in early 2017.
Combined with coral bleaching - which is predicted to become more frequent and more severe as a result of steadily rising ocean temperature - the long-term trend of coral decline is expected to continue and accelerate.
Coral bleaching occurs when abnormal environmental conditions, like heightened sea temperatures, cause corals to expel tiny photosynthetic algae, called 'zooxanthellae'.
The loss of these colourful algae causes the corals to turn white, and bleach. Bleached corals can recover if the temperature drops and zooxanthellae are able to recolonise them, otherwise the coral may die.
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