A Chinese boat that crashed into a protected coral reef in the Philippines was hiding the remains of a second environmental disaster in its hold: thousands of illegally killed pangolins, a scaly anteater prized for its meat and scales in China.

The vessel hit an atoll on 8 April at the Tubbataha national marine park, a Uuneso-designated World Heritage site on Palawan island that was also struck by a US minesweeper in January. Coastguard spokesman Armand Balilo said on Monday about 400 boxes, totalling over 10 tonnes of frozen pangolins, were discovered during a second inspection of the boat on Saturday.

All trade in the four Asian species of pangolin has been illegal since 2002 but the appetite of Chinese consumers for its meat, prized as a delicacy, and its scales, believed to benefit breast-feeding mothers, has virtually wiped out the creatures in China, Vietnam, Laos and Cambodia. Pangolin traders, who use dogs or traps to capture the wild animals, have since moved into its last habitats in Java, Sumatra and the Malaysian peninsula, driving populations down but prices up.

Chris Shepherd, an expert at wildlife trade group Traffic and based in Malaysia, told the Guardian: "There is no way a slow-breeding species like the pangolin can withstand this huge pressure for long." He said the enforcement of laws had not kept pace with demand for the pangolin meat and scales, which can fetch hundreds of dollars per kilogramme in China: "We have seen a really obscene amount of seizures but very few people are arrested and even fewer convicted."

The 12 Chinese crewmen from the wrecked vessel are being held on charges of poaching and attempted bribery, said Adelina Villena, the marine park's lawyer, and face further charges, including damaging coral reef and possessing pangolin meat. Tubbataha reef is a marine sanctuary and popular diving destination 640km south-west of Manila and had already been damaged by a US navy ship that got stuck in January and had to be dismantled.

The Philippine military quoted the fishermen as saying they accidentally wandered into Philippine waters from Malaysia. The fishermen face up to 12 years' imprisonment and fines of up to $300,000 (£196,000) for the poaching charge alone. For possessing pangolin meat, they can be imprisoned up to six years and fined, Villena said.

The Philippine pangolin haul is one of the largest on record. In 2010, 7.8 tonnes of frozen pangolin and 1.8 tonnes of scales were seized from a fishing vessel by customs officers in Guangdong, China, while a series of customs seizures in Vietnam in 2008 yielded 23 tonnes of frozen pangolins in a week.

It is not yet clear from which of the four Asian pangolin species the meat comes. The International Union of Conservation of Nature lists two species as endangered: the Sunda, or Malayan pangolin, and the Chinese pangolin. Two others, including the Philippine pangolin endemic to Palawan, are classified as near threatened, though the Philippine government considers its pangolin threatened because of the unabated illicit trade. Overall, the IUCN says rising demand is wiping out pangolins from their forest habitat in south-east Asia, along with many other species, leaving "ghost forests" stripped of wildlife. In 2007, an abandoned 'Noah's Ark' of 5,000 rare animals was found floating off the coast of China.

"The enforcement agencies in the region are very reactive," said Shepherd. "There is not enough investigation into who is behind the networks." In March, the world's top wildlife trade official told the Guardian that crime syndicates and terrorists are outgunning those on the frontline of wildlife protection and pose a deadly threat to both people and animals.