WWF-Australia Head of Oceans, Richard Leck, added: "Scientists warned that without sufficient emissions reductions we could expect annual mass bleaching of the Great Barrier Reef by 2050".
The bleaching is part of a global event affecting the world's coral reefs over the past two years.
This event is right in the tourism heartland and it's a 6.4 billion dollar industry employing 63,000 people in the catchment of the great barrier reef.
The Greenpeace findings are backed by Terry Hughes from James Cook University's Centre of Excellence for Coral Reef Studies, who called the second bleaching event the "worst kept secret in the world".
"Importantly, not all bleached coral will die".
"Just a few months ago, these corals were full of color and life".
"There is no doubt that if we do not get our act together globally we will have serious damage to the barrier reef, we could see the barrier reef lose a huge amount of biodiversity, when you look at the Cayman islands they have about 30 species of coral and we have 300".
The coral may die in the six to 12 months after bleaching, meaning the level of mortality on the reef will not be determined until later in the year.
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"What's happening with global warming is that these events are becoming the new normal", he told BuzzFeed News. They will survey 1150 reefs along the stretch again.
Documentation of the Great Barrier Reef near Port Douglas from Greenpeace Australia Pacific, shows damage of coral.
"We are working closely with the Commonwealth to ensure we gather all the information required to determine the extent of this latest bleaching event", Mr Miles said.
He said indications from underwater thermometers were that although sea surface temperatures were lower than this time last year, they had been above average over the last year, including through winter.
Coral bleaching occurs when corals expel the algae living in their tissues when water is too warm. If oceans warm 2.7°F, it will essentially be a death sentence for most coral. However, it is believed that the site remains on the organisation's "watch list".
The Australian and Queensland governments, which are obliged to show how they are jointly managing the reef's long-term conservation, acknowledge climate change is its main threat.
Environmental groups are acting against the proposed construction of the largest coal mine in Australia, which could significantly contribute to the greenhouse gas emissions.
However, the federal environment minister, Josh Frydenberg, at the start of a review of the government's climate change policies earlier this year, was forced to rule out pricing carbon after a brief internal revolt.