With announcements to fight the decision, Australian Environment Minister Sussan Ley says the challenges are being adhered to regularly and that Australia is being "singled out".
"We were blindsided by a sudden late decision," Ley said.
The World Heritage Committee will consider the draft recommendation when hosting a meeting in China next month.
"It is almost unheard of for a site to be added to the endangered list, or recommended ... without the necessary consultation leading up to it.
Member of Leichhardt, Warren Entsch was also surprised by the claims, saying the reef is in good health.
"We have never been more on top of crown of thorns than we are know. Wonderful organisations like the Reef of Rainforest Research Centre do amazing work." Entsch said.
Ley explained that while climate change is one of, if not the greatest risk to the reefs stunning beauty, but places an argument that action is being taken.
With Australia being urged to take "accelerated action" on global warming, the draft recommendation comes in the midst of a longstanding dispute between the federal government and UNESCO over the status of the coral landscape.
The reef stretches over 2,300km off the north-east coast, gaining World Heritage rank in 1981.
Scientists say a glaring issue is the rise in sea temperatures, caused by the burning of fossil fuels.
"The recommendation from UNSECO is clear and unequivocal that the Australian government is not doing enough to protect our greatest natural asset, especially on climate change," Head of Oceans for Nature-Australia, Richard Leck.
The potential downgrade to 'in danger' will be assessed by relevant world environment officials, and steps will be taken to sustain any risk.
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