The 2,300-kilometre (1,400-mile) World Heritage-listed reef suffered its most severe bleaching on record last year due to warming sea temperatures during March and April.
Initial aerial and in-water surveys showed 22 percent of shallow water corals were destroyed in 2016, but it has now been bumped up to 29 percent and with the reef currently experiencing an unprecedented second straight year of bleaching, the outlook is grim.
"We're 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," Great Barrier Reef Marine Park Authority (GBRMPA) chairman Russell Reichelt said.
"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's expected we'll also see an overall further coral cover decline by the end of 2017."
Bleaching, which occurs when abnormal conditions such as warmer sea temperatures cause corals to expel tiny photosynthetic algae, draining them of their colour, also extended to deeper corals beyond depths divers can typically survey.
But mortality of those reefs could not be systematically assessed.
The most severely impacted region was an area north of the popular tourist town Port Douglas, where an estimated 70 percent of shallow water corals have died.
Cairns and Townsville, also hugely popular tourist destinations, are among the regions hardest-hit from the 2017 bleaching event, although southern parts of the natural wonder escaped the worst.
Corals can recover if the water temperature drops and the algae are able to recolonise them, but it can take a decade.
Reichelt said the storm impacted a quarter of the reef but a complete picture for 2017 would not be available until next year.
The GBRMPA hosted a summit last week of more than 70 of the world's leading marine experts to work on a blueprint on how best to respond to the threats.
Among options explored was developing coral nurseries, strategies to boost culling of crown-of-thorns starfish, expanding monitoring systems and identifying priority sites for coral restoration.
Key to the talks was the need to slash greenhouse gas emissions to prevent warming sea temperatures.
"The Great Barrier Reef is a large and resilient system that's previously shown its capacity to bounce back, however the current changes are undermining the resilience of the reef," said Reichelt.
"Summit participants voiced their strong concern about the need for global action to reduce greenhouse gas emissions, the driver of climate change."
The world's nations agreed in Paris in 2015 to limit average warming to two degrees Celsius (3.6 degrees Fahrenheit) over pre-industrial levels, by curbing fossil fuel burning.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)
Get Breaking news, live coverage, and Latest News from India and around the world on NDTV.com. Catch all the Live TV action on NDTV 24x7 and NDTV India. Like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.