Coral "bleaching" has led to widespread coral decline and habitat loss on the world's largest coral reef system.
Surveys show that 29% of corals died in 2016, greater than the  figure of 22% projected in mid-2016.
The worst-hit area was near Port Douglas, where 70% of shallow water corals died, but there was a recovery of corals in the south of the reef.
The latest results come from surveys carried out by the Marine Park Authority, Queensland Parks and Wildlife Service, Australian Institute of Marine Science and the ARC Centre of Excellence for Coral Reef Studies.
Great Barrier Reef Marine Park Authority chairman Russell Reichelt said: "As has been the case with reefs across the world, the Great Barrier Reef has experienced significant and widespread impacts over the last two years.
"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."
According to newpaper reports, a meeting over the reef's future was recently told that the federal and Queensland government's long-term plan to protect the reef, announced in 2015, was no longer achievable.
Bleaching occurs when the algae living on coral is expelled due to stress caused by extreme, sustained changes in temperature. This turns the coral white.
In 2017, further coral die-offs are expected from the second year of bleaching in a row, and the impacts of tropical cyclone Debbie, the officials said.
Researchers say that climate change is a significant driver behind the coral loss and experts have said the window is closing fast to cut the greenhouse gas emissions pushing up temperatures and harming the reef.

Portsmouth Police tweeted residents took refuge on the roof of the building while awaiting rescue.
People were told to avoid the area as firefighters from Hampshire Fire and Rescue worked to get the blaze on the fourth floor under control.
The fire was put out shortly before 15:00. Hampshire Fire and Rescue tweeted "everyone was safe".
The people on the roof were advised to wait until the smoke had dispersed to come down.
The fire service said it is believed the fire started in the kitchen.
An onlooker tweeted it was "chaos" in the area as the car park at Gunwharf Quays - a waterfront shopping outlet - was closed.
People living in nearby buildings were advised to keep windows and doors shut.

A number of houses were evacuated after the device was discovered on Ainsworth Avenue off the Shankill Road.
The security alert has now ended.
Police have appealed for information about the incident.
Democratic Unionist Party MLA William Humphrey said those behind the device had been "utterly reckless".
"This criminal act of madness will be condemned by all right-thinking people," he added.

The museum hopes to raise £5m to develop its Maryfield tram depot into a fully-restored national visitor attraction.
It has been based at its temporary headquarters in Market Street since April 2014.
The grant will fund a new museum director and consultancy post for two years.
The museum's chairman Jimmy McDonell said: "We are extremely privileged to have been offered this grant from the Mathew Trust.
"It will allow us to carry the project forward by bringing in the expertise we need to make the very best of this opportunity that we have."
The museum, which is run by volunteers, attracted more than 10,000 visitors in its first year.
VisitScotland regional director Jim Clarkson said: "In Scotland's Year of Innovation, Architecture and Design, the grant will help Dundee Museum of Transport remain an exciting part of the city's tourism offering, boosting the visitor economy in the process."
Australia's Great Barrier Reef lost nearly a third of its corals in the past year, officials have said.
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Firefighters tackled a large fire in a high-rise building in the Gunwharf Quays area of Portsmouth.
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Police have said a suspicious object found in west Belfast was a "crude but viable" bomb.
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Dundee Museum of Transport's fundraising campaign has received an £80,000 grant.