A large carrier ship ran aground and damaged three hectares of coral reefs in a popular diving area and marine protected area just off Malapascua Island in the central Philippines last week. The area, called Monad Shoal, is near important habitat for endangered thresher sharks. Government scientists are surveying the area to assess the damage.

National Geographic underwater photographer David Doubilet documented the damage to the reef in rarely seen photos.

"This is a key, key reef and it's about the only place where you can see thresher sharks," Doubilet says.

Thresher sharks use their scythe-like long tail fins to hunt, lashing out at schools of prey fish in fast, aggressive attacks. There are three known species, and one, the pelagic, is found around the Philippines. The sharks spend most of their time hunting in deep water, where they are rarely seen, but at dawn they often surface to have their skin cleaned of parasites by pea-sized animals called copepods.

Several of these "cleaning stations" are used by the sharks around Monad Shoal. These important areas were very close to the boat strike but were not directly hit, says Doubilet, who notes that thresher sharks are listed as vulnerable to extinction by the IUCN.

The Panama-registered Belle Rose hit the reef about four nautical miles from Malapascua Island, a popular dive tourism destination and shark sanctuary. The 600-foot (183-meter) long vessel was loaded with 48,000 tons of cement powder and was reportedly en route from Nantong, China, to Cebu, Philippines, according to the Maritime Herald.

Due to alleged human error, the Herald reports, the ship smashed into the reef, causing significant damage to its hull. The vessel took on water but did not sink and reportedly did not leak any oil or other material into the sea. Other ships came to its aid and were able to transfer the cargo off and prepare it for transport to the nearest port, which was completed on June 20.

Doubilet's photos show scrape marks on the bottom of the hull as well as damage to the coral. A survey is being done to assess the loss of marine life along the damaged zone, which is estimated at 1,585 feet (483 meters) along the shoal. (Learn about how a billionaire conservationist's yacht damaged a coral reef.)

The thresher sharks are a major draw for thousands of tourists to the area and nearby Daanbantayan town.

View Images Deep scrape marks are visible on the bottom of the Belle Rose, where it dragged over fragile coral. Photograph by David Doubilet, National Geographic

"Many people there depend on tourism for their livelihood," Doubilet says. "That in turn makes them very visible and valuable and helps protect them, to keep them swimming in a sea where they need to be."

Although ship strikes are a known hazard to coral reefs—which have experienced unprecedented bleaching this summer from warm waters—actually photographing the impact isn't common. Much ship damage occurs far away from human habitation, so recording it can be tricky.

In this case, the accident happened in an accessible (and protected) area that is also well known by divers. Further, Doubilet had just been at the cleaning stations documenting the sharks on assignment. When the ship ran aground, he was on his way to Manila, but turned around to record the incident.

The Philippines coast guard is investigating the incident. It's unclear what legal action may result.

The Belle Rose was built in 2011 in Japan and is reportedly owned and operated by Japanese company Sunship Management, according to the Herald. The crew of eight officers and 12 members reportedly hailed from the Philippines.