Japan's biggest coral reef has not recovered from bleaching due to rising sea temperatures, with only one percent of the reef in a healthy condition, according to a government study.

The overall volume of coral in Sekisei Lagoon in southwestern Japan near Okinawa had already plunged by 80 percent since the late 1980s due to rising water temperatures and damage caused by coral-eating starfish.

Now only 1.4 percent of the lagoon, which stretches over 67.89 square kilometres, is in a healthy condition, the environment ministry said, after it was hit by mass bleaching in 1998, 2001, 2007 and most recently 2016.

"If coral reefs don't recover, it means a loss of rich fauna for a variety of creatures and would have grave impact on the ecosystem in the region," ministry official Chihiro Kondo told AFP on Friday.

For the first time since 2008, the ministry analysed satellite photos and information from some 1,000 monitoring sites for the Sekisei Lagoon and two other reefs around the Ishigaki and Iriomote islets in Okinawa.

The ratio of healthy corals stood at 14.6 percent in 1991 but dropped to 0.8 percent in the 2008 survey, Kondo said.

Two other neighbouring lagoons had similar results with the ratio of healthy areas around one percent.

Bleaching occurs when abnormal environmental conditions, such as warmer sea temperatures, cause corals to expel tiny photosynthetic algae, draining them of their colour.

Corals can recover if the water temperature drops and the algae are able to recolonise them.

"But the latest study shows that corals haven't recovered much since 2008, presumably partly because of the 2016 bleach," Kondo said.

One of the worst mass bleaching episodes on record took place in 1998 when the El Nino phenomenon was exceptionally strong, affecting reefs in 60 tropical countries.

Coral reefs are also under pressure from ocean acidification linked to CO2 emissions, scientists warn.

Corals make up less than one percent of Earth's marine environment, but are home to more than 25 percent of marine life.

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