A report by the Global Coral Reef Monitoring Network said the natural biodiversity of coral reefs was under threat.
While praising conservation efforts, the group warned "our attempts at managing coral reefs to arrest their decline are still lagging behind the increasing rate of reef degradation."
The report found that over-fishing, pollution, sedimentation and activities such as dredging were threatening more than a quarter of the world's coral reefs.
But it identified bleaching caused by rising sea temperatures as the major danger, saying up to 40 percent of reefs were directly at risk.
Bleaching drains corals of their distinctive colours and often kills them completely, leaving white husks that eventually break down into rubble on the sea floor.
However, the report found that Australia's Great Barrier Reef and other reefs protected by conservation zones and proper scientific management, were in better health than most of their counterparts around the world and appeared to recover well from bleaching.
Australian Institute of Marine Science (AIMS) researcher Clive Wilkinson compiled the report from contributions by 151 scientists in more than 100 countries.
He said scientists had already received a "wake-up call" about human activities destroying coral reefs when the largest coral bleaching and mortality event on record temporarily destroyed about 16 percent of the worlds reefs.
Wilkinson said there was a real risk that coral reefs would become the first major marine ecosystem impacted by global warming.
He said more than 400 reefs were hit by bleaching in 2002 and there were doubts about their ability to recover from continued attacks.
"This season will be telling. A collapse in the monsoon, an absence of trade winds and the clear skies associated with another El Nino will weaken corals," he said.
"Put an infusion of fresh water from a possible cyclone on top of that and you have trouble."
Other problems included nutrient runoff, infestation by the coral-eating crown of thorns starfish and over-exploitation of reef resources.
AIMS scientist Terry Done said it was unclear how quickly coral could adapt to warmer terperatures.
"They will adapt and find a new equilibrium over time but it could take hundreds of years, " he said.
"Meanwhile, in 20 years some of thise reefs could look pretty ugly."