The regional organisation, the Pacific Community, says high water temperatures in the Pacific are making the "third global coral bleaching" event even worse.
In 2015, the United States' National Oceanic and Atmospheric Administration declared the third ever global coral bleaching event, describing the problem as worse than the 1998 disaster when 16 percent of the world's reefs were killed.
Thirty-eight percent of reefs are under threat and over 12,000 square kilometres of reefs will be killed according to the Pacific Community's Brad Moore.
Mr Moore said the El Niño weather pattern and the high temperature of the water is also killing fish, causing thousands to be washed up in Fiji and Vanuatu.
He said the impact on coral will in turn be felt in the fisheries.
"Corals are the foundation species of the reef, so they provide food, provide shelter for many species, so essentially without corals we will lose our fisheries. And coral reefs also provide coastal areas protection from waves and from storm damage."