However, the World Heritage Committee opted not to include it during its annual meeting in Poland, a move praised by the Australian government as a "big win," but condemned by campaigners as "farcical."
UNESCO's List of World Heritage in Danger has 55 entries, which include natural wonders and man-made sites. Jerusalem's Old City was added in 1982, and Aleppo, the Syrian city bombarded by air strikes, made the list in 2013.
"We've received a strong endorsement that our Reef 2050 plan, which is a coordinated, integrated plan with the Queensland Government, is working," added the minister.
Anna Marsden, managing director of the Great Barrier Reef Foundation said that the decision was "welcome" but said that, with the fate of the entire reef at stake, more needs to be done.
"We welcome this decision from UNESCO which recognizes much is being done to reduce pressures on the Great Barrier Reef -- however with so much to lose, more needs to be done," she said.
"It is clear everyone must step up and do more to protect our global treasure."
'Perplexing;' 'farcical' decision
Placed on the World Heritage List in 1981, the Great Barrier Reef is a major victim of climate change.
As the oceans continue to warm, the fragile corals that constitute the reef continue to die, leaving in their place a graveyard of white, lifeless stalks.
The acidification of the oceans, a process caused by dissolved atmospheric carbon dioxide -- another byproduct of industrialization -- adds to the weakening of corals.
UNESCO's own report on coral ecosystems, released in June, states that "soaring ocean temperatures in the past three years have subjected 21 of 29 World Heritage reefs to severe and/or repeated heat stress, and caused some of the worst bleaching ever observed at iconic sites like the Great Barrier Reef."
David Booth, Professor of Marine Ecology at University of Technology Sydney and past President of the Australian Coral Reef Society, said that the decision to leave the ecologically fragile formation was "perplexing."
"The Great Barrier reef is under extreme threat from climate change, coal development, overfishing and influx of nutrients and the lack of UNESCO recognition of the danger it is in is perplexing."
Melbourne-based climate activist David Spratt called the decision "farcical," given the extent of the Reef's die-off.
More than two-thirds of the coral in the reef is experiencing "shocking" amounts of bleaching, aerial surveys released in April revealed.
Environmental group Greenpeace pointed the finger at the Australian government for not doing enough to combat climate change.
"The government says one thing, but does another on the reef," said Greenpeace campaigner, Alix Foster Vander Elst, in a statement released by the group.
"When the government is spending 55 times more on fossil fuel subsidies than on its much-touted Reef 2050 plan, it's quite clear what its priorities really are.
"What we should be doing is cutting fossil fuels subsidies, banning new coal mines and offering the world real climate leadership."