A Chinese fishing vessel has crashed into one of the Philippines' most famous reefs and damaged thousands of square metres of centuries-old coral, the marine park has said.

Some 3,902 square metres of coral was destroyed after the boat became stranded in the Tubbataha marine park, a UNESCO World Heritage-listed coral reef, the park management said on Saturday.

"The damage the Chinese vessel caused to the reef is heart-breaking," Angelique Songco, the head of the marine park said in a statement after experts assessed the affected area.

Some of the coral destroyed by the Chinese vessel was 500 years old, Songco said, adding that the damage was much larger than the area destroyed when a US Navy minesweeper, the USS Guardian, got stranded on Tubbataha in January.

The 48-metre vessel, carrying 12 suspected Chinese fishermen, plowed into the Tubbataha Reef near the western island of Palawan on April 8.

Authorities later found hundreds of dead pangolins, an internationally-protected species, hidden inside the vessel.

Tubbataha marine park information officer Glenda Simon told the AFP news agency that the 12 Chinese would likely be fined about $2.32m just for trespassing into the marine park and destroying the coral.

The government has already charged them with poaching and they could face an additional 12 to 20 years in jail for possession of the pangolins in violation of wildlife law.

Pangolins are widely hunted in parts of Asia for their meat, skin and scales and in China they are considered a delicacy and to have medicinal qualities.

The Philippine office of the World Wide Fund for Nature condemned the poaching of the pangolins after the men were caught, saying that growing demand in China was wiping the animal out in Southeast Asia.