Nowadays, these world class reefs are being destroyed at a faster rate. Tsunami which occurred in Indian Ocean destroyed most of the reefs along the western coast of Sumatra island. In South East Maluku and North Maluku islands, hundreds of trawlers catch fish. Most of them are equipped with shrimp nets that catch fish and shrimp on the bottom of the sea. While many countries are restricting the bottom trawling practices, Indonesian seem to ignore them.
Coral reefs in Banda islands and South East Molucan islands have been dying for years from poisonous tailing produced by Freeport, the largest copper mine company in the region. Sea water which has been contaminated by this tailing has even threatened Great Barrier Reef in Australia.
Most of the coral reefs in Kepulauan Seribu have died since tens of years ago due to coastal development, sedimentation and debris from Jakarta, the capital city of the state.
People believe that reefs in Bali and Bunaken of North Sulawesi are still in good condition. In fact, the reefs in those islands are being damaged by debris from Manado city and some tourism activities. Many of the physical damages of reefs in Bunaken National Marine Park are caused by anchors and divers and snorkelers, as well as swimmers. Some recreational divers touch and turn corals or turtles. Many hotels or resorts built along the beach do not have sewage water treatment systems that are required to process and filter the wastes before being discharge to the environment.
Papuan coral reefs are not excluded in this case. The Geelvink coral reefs which have been in pristine for hundreds of years are facing threats from soil sediments. These sediments flow during the raining season from riverbanks. Rapid deforestation of Papuan forest cause more mud flood that flows to the sea. The mud covers sea grasses and reefs which are the source of food of fish.
From 1942 to 1944 West Papua was the battle ground US and Japanese troops. Both sides dropped thousands of bombs, laid sea mines and torpedoed ships. Today sunken ships, and unexploded ammunition still pose potential threats coral reefs in the Papuan and other Pacific islands.