Launched at the International Coral Reef Symposium in Cairns, it said the threat was substantially more than the global average of 60% and urged greater efforts to reduce destructive fishing and run-off from land.
"When these threats are combined with recent coral bleaching, prompted by rising ocean temperatures, the percent of reefs rated as threatened increases to more than 90%," the report said.
The Coral Triangle covers Indonesia, Malaysia, Papua New Guinea, the Philippines, The Solomon Islands, and East Timor and contains nearly 30% of the world's reefs and more than 3 000 species of fish.
More than 130 million people living in the region rely on reef ecosystems for food, employment, and revenue from tourism, according to Reefs at Risk Revisited in the Coral Triangle.
"Across the Coral Triangle region, coastal communities depend on coral reefs for food, livelihoods, and protection from waves during storms, but the threats to reefs in this region are incredibly high," said lead author Lauretta Burke.
"Reefs are resilient - they can recover from coral bleaching and other impacts - particularly if other threats are low.
"The benefits reefs provide are at risk, which is why concerted action to mitigate threats to reefs across the Coral Triangle region is so important."
The report by the World Resources Institute, in collaboration with environmental groups WWF, The Nature Conservancy and Conservation International, will be used by the six countries to develop their management of the reefs.
"[The report] is an important contribution for supporting the six Coral Triangle countries in making critical decisions related to protecting their marine resources," said Maurice Knight, a contributing author.
"The region-wide perspective on the status of coral reefs as depicted in this report demonstrates the urgency of the situation and the need for immediate action."
The International Coral Reef Symposium, held every four years, has attracted more than 2 000 scientists from 80 countries to present the latest advances in coral reef conservation.
Their research and findings are considered fundamental to informing international and national policies and the sustainable use of coral reefs globally.