(CNN) -- China has urged the Philippines to "guarantee the safety and legitimate rights" of fishermen who have been taken into custody for poaching after their vessel ran aground on the protected Tubbataha Reef -- the latest incident in often tense relations among nations in the South China Sea.

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Foreign Ministry spokesperson Hong Lei made his comments on Thursday, state-run Xinhua reported, a day after Philippine authorities formally charged 12 fishermen with poaching and attempting to "corrupt public officials," the Tubbataha management office said in a news release.

The 12 Chinese nationals were arrested on April 8 after their ship ran aground on the reef. The fishermen also faced administrative charges for for illegally entering Tubbataha Reefs Natural Park and for damage to the reefs. Crews will be sent to remove fuel from the 500-ton vessel to attempt to float it off the seabed, according to park authorities.

The coral reef was the same that a U.S. Navy minesweeper ran aground and damaged the reef on January 17. Earlier this week, Philippine officials said they would be sending the U.S. governmenta $1.5 million bill for damage to the reef.

Tubbahata Reef is a UNESCO World Heritage site that is home to about 500 species of fish and 350 species of coral as well as whales, dolphins, sharks, turtles and breeding seabirds.

Elsewhere in the region, an agreement between Japan and Taiwan on fishing rights among disputed islands in the East China Sea has angered Beijing. Lei told reporters Beijing is China is "seriously concerned" about the fishery agreement, Xinhua reported.

The islands -- known as Senkaku in Japan and Diaoyu in China -- is a periodic flashpoint between Tokyo and Beijing, which have competing claims to ownership. Anti-Japanese demonstrations in China turned violent last September, with Japanese businesses and cars damaged, dragging relations between Asia's two largest economies to their lowest level since World War II.