The report into the management of the reef, released on Saturday, warns the reef could be listed as a World Heritage site in danger unless substantial changes are made to Australia's management of the area.
It says the Australian Government needs to implement a strategic assessment before considering future developments around the reef.
Greenpeace spokesman John Hepburn says the governments need to consider the recommendations very closely.
"The UNESCO report is really a damning indictment on the threat posed to the Great Barrier Reef by coal port developments and gas port developments in Queensland," he said.
"Really what they are saying is if we continue with business as usual, then they are going to have to list the Great Barrier Reef as in danger."
The report recommends an independent review into the management of Gladstone Harbour and Curtis Island, saying action is needed to secure the reef's long-term conservation.
Australia's Environment Minister Tony Burke says there have been challenges for the Great Barrier Reef which have been "mounting for some time".
"The Great Barrier Reef has been at a crossroads," he told reporters on Saturday.
"Changed practices still have a way to go and there's a call from UNESCO in this report for us to continue that work."
Mr Burke says he will discuss the impact on the Gladstone Harbour with the Queensland Government.
But he says there needs to be a balance between protecting the reef and maintaining tourism in Queensland.
"I reckon anyone who wanted to undo all the tourism operations in the Whitsundays in the name of keeping the area pristine would quite rightly have a lot of people saying, hang on, we want to make sure that something as magnificent as the Great Barrier Reef can be enjoyed and seen by the people of the world as well," he said.
"There is a way of having sustainable development. This report is saying look at the whole area strategically and we agree that is the correct approach."
Greens Senator Larissa Waters welcomes the UNESCO report and says it is what her party has been calling for.
She says the reef could be on the danger list within eight months if things do not improve.
"This really is an explosive report, it's a slap in the face for the Queensland and the Australian governments who've been thumbing their nose at the reef and treating it effectively like a coal and gas highway and a rubbish dump for dredging," she said.
"It's about time we start treating it like a world heritage icon or we're going to lose it."
The World Wildlife Fund says the report is a strong wake-up call and governments need to act.
"They want to see a halt on permitting new development outside the established port areas so that's a fairly strong message for the government," conservation manager Gilly Llewellyn said.
"If they don't see that substantial progress then they're going to be calling for consideration to be listed on World Heritage in Danger next year."