A boatman paddles away from the Sarangani, a ship on which archaeologists became embroiled in a standoff with China, in Manila Bay. Jeremy Page/The Wall Street Journal
Underwater archaeologist Franck Goddio's team was exploring the wreckage of a 13th-century Chinese junk off the coast of the Philippines when it made an unwelcome discovery about China's maritime muscle in the 21st century.
As a twin-prop plane swooped overhead, a Chinese marine-surveillance vessel approached the team's Philippines-registered ship and began broadcasting instructions in English over a loudspeaker.
"They said this area belonged to the People's Republic of China, and they told us to scram," recalls one of the people on board last year. "It was pretty scary." Chinese officials confirm the incident took place but say the archaeologists' mission was illegal.
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With territorial disputes escalating in the waters off China, the Chinese government has begun asserting ownership of thousands of shipwrecks within a vast U-shaped area that covers almost all of the South China Sea, which it says has been part of its territorial waters for centuries.
China has ordered its coast guard to prevent what it considers illegal archaeology in the waters it claims, and it is pouring money into a state-run marine-archaeology program. Chinese archaeologists are preparing their first comprehensive survey of undersea sites, including in disputed areas.
Chinese officials say their efforts will curb the theft and treasure hunting they say has destroyed numerous sites and flooded the global market with looted Chinese antiquities.

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There is a political dimension to China's plans. Chinese archaeologists openly aspire to bolster their country's historical claims to the contested South China Sea, which overlap with those of Vietnam, Malaysia, Brunei, Taiwan and the Philippines.
"We want to find more evidence that can prove Chinese people went there and lived there, historical evidence that can help prove China is the sovereign owner of the South China Sea," says Liu Shuguang, head of the Chinese government's Center of Underwater Cultural Heritage, set up in 2009 to oversee underwater archaeology in the country.
Tensions have been running high in the region over China's intensifying campaign to assert territorial claims, not only in the South China Sea, but in the East China Sea, which is contested by Japan. On Nov. 23, China proclaimed a new air-defense identification zone over islands claimed by both China and Japan but controlled by Tokyo.
The South China Sea, one of the world's busiest trading routes, is littered with wrecks from the last two millennia, including Chinese junks, Indian and Arab dhows, Dutch and British trading schooners and World War II warships. Chinese archaeologists say they have gathered coordinates for 70 shipwrecks in those waters but estimate there are at least 2,000, and possibly many more.
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A team working with French underwater archaeologist Franck Goddio, shown in 2010, was exploring the wreckage of a 13th-century Chinese junk off the coast of the Philippines when a Chinese marine-surveillance vessel ordered them to leave the area. Associated Press
In the early 15th Century, the Ming dynasty's Yongle Emperor dispatched an unprecedented series of naval expeditions to the Indian Ocean. Commanding them was a eunuch admiral known as Zheng He.
Mr. Goddio, a Frenchman who is one of the world's leading marine archaeologists, had worked in the area since the 1980s, excavating 15th-century Chinese junks, 16th-century Spanish galleons and 18th-century British merchant ships. In addition to the trip last year, his team had visited the cluster of reefs and rocks off the Philippines, called the Scarborough Shoal, in 2011. Both expeditions were part of a joint research project with the National Museum of the Philippines, which collaborates with foreign archaeologists because of a shortage of state funding.
Different countries refer to the disputed islands by different names.
People involved in the project say it has no political or commercial agenda. During last year's trip, they say, they were examining pieces of celadon, a form of green-glazed ceramic, from a wreck that long ago broke apart on the sharp coral.
Chinese officials see ulterior motives.
"The Philippines sent some French archaeologists to do what? To drag away this shipwreck," says Mr. Liu of China's Center of Underwater Cultural Heritage. "Because this was material evidence that Chinese people first found the Scarborough Shoal, they wanted to destroy evidence that was beneficial to China." The archaeologists deny that.
Chinese archaeologists haven't started excavating sites at the Scarborough Shoal, but they have begun work on Chinese wrecks around the Paracel Islands, which lie about 200 miles from the coasts of China and Vietnam and are claimed by both countries. China has controlled the islands since 1974, when it defeated Vietnam in a brief naval battle.
A stone statue in Nanjing of Chinese voyager Zheng He, who sailed an armada of treasure ships as far as Africa about 600 years ago. The admiral is celebrated in China as the face of an era when it projected power far beyond its shores. Imaginechina/Agence France-Presse/Getty Images
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Mike Hatcher prepares to dive from his ship in the South China Sea in 1986. On the expedition he found the 'Nanking cargo,' a haul of Chinese porcelain and gold from the wreck of the Geldermalsen, an 18th-century Dutch East India Co. ship that raised more than $20 million at auction in Amsterdam. Associated Press
"Marine archaeology is an exercise that demonstrates national sovereignty," Li Xiaojie, the vice minister of culture, was quoted as saying by state media in September 2012 as he examined porcelain retrieved from a wreck off the Paracels.
Chinese archaeologists say the survey encompassing other disputed areas will begin this year or next.
They also say they hope to support the government's efforts to re-establish China as a world maritime power, by focusing their research on the "Maritime Silk Road," which connected China by sea with India and Africa beginning in about the second century B.C.
China's five-year plan for 2011 to 2015 calls for the government to promote a seafaring heritage embodied by Zheng He, a eunuch admiral who sailed an armada of treasure ships as far as Africa about 600 years ago. The admiral is celebrated in China as the face of an era when it projected power far beyond its shores.
Xi Jinping, China's new president, has repeatedly emphasized the importance of maritime power—at times invoking Zheng He—as part of a vision to reclaim China's world prominence.
Zhang Wei, one of China's first underwater archaeologists, says the nation is "extremely focused on being a great and strong maritime power," which he calls the "grand backdrop" to China's marine-archaeology program. The program was launched, he says, under the auspices of President Xi's father, who served as vice premier under Deng Xiaoping in the 1980s.

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Two enameled globular teapots painted with peony and bamboo below a border of trellis-pattern; the porcelain survived the wreck and lasted more than two centuries under the sea so well because it was packed inside the tea, which in turn was in wooden chests. Christie
CLICK TO SEE SLIDESHOW: See some of the porcelain and gold salvaged after more than two centuries from the sunken merchant ship Geldermalsen—and sold at auction in 1986 for over $20 million.
Mr. Zhang says interest was kindled by commercial treasure hunters who operated in the South China Sea. Among the most famous was Mike Hatcher, a Briton whose haul of Chinese porcelain from the wreck of the Geldermalsen, an 18th-century Dutch East India Co. ship that sank in the South China Sea, raised more than $20 million at auction in Amsterdam in 1986.
Chinese leaders dispatched two officials to that auction to try to buy some of the items with cash, according to Mr. Zhang. "They only took about $30,000, and they couldn't buy a single thing," he says.
China's National Museum established its Underwater Archaeology Center the following year and appointed Mr. Zhang to head it—mainly, he says, because he was one of the few Chinese archaeologists who could swim.
The first big find in Chinese waters—a roughly 800-year-old merchant ship named the Nanhai One—was made in 1987 while a British salvage company was searching for a Dutch East India Co. wreck. The British team was forced to withdraw after the Nanhai One was identified as a Chinese ship.
Since then, there has been almost no foreign participation in marine archaeology in China, according to Chinese and foreign archaeologists. And only Chinese wrecks have been excavated in Chinese waters.
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A replica of a treasure ship sailed by Zheng He about 600 years ago at a museum in Nanjing. Getty Images
Chinese authorities, meanwhile, have trained more than 100 marine archaeologists, built at least three underwater-archaeology museums and invested millions of dollars in research. On Thursday, they announced a new project to remove up to 80,000 artifacts from the Nanhai One, which was lifted off the seabed in 2007 and placed in a water tank in a museum.
Next year, China plans to launch a 184-foot ship designed for marine archaeology, the first of its kind in the country, according to state-media reports.
China also is funding joint projects in other countries' waters, focusing mostly on locating wrecks linked to Zheng He. Last year, Chinese archaeologists using sonar identified five wrecks they believe were part of his fleet in the Gulf of Oman and the Strait of Hormuz, according to Chinese state media.
One reason Chinese authorities are so interested in tracing Zheng He's travels is that he is said to have visited several rocks and islands in the South China Sea.
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Chinese archaeologists work with porcelain artifacts from the Nanhai One shipwreck, which dated back to the Southern Song Dynasty (1127-1279), in a structure in Yangjiang, China, in 2009. Imaginechina/Agence France-Presse/Getty Images
Foreign experts say they welcome China's new willingness to invest in underwater archaeology and relish the prospect of learning more about sites in China's waters.
But some say they are concerned that a political agenda might be driving China's choice of sites, its exclusion of foreign archaeologists and its relative lack of openness about its research.
"There's this strong sense of nationalism that flows through the Chinese program," says Jeffrey L. Adams, an anthropologist at the University of Minnesota who has written about Chinese archaeology.
Foreign archaeologists mostly agree that Chinese-built ships and cargo account for many of the sites in the South China Sea because of the international trade in Chinese porcelain and silk.
But many of the wrecks lie far from the Chinese mainland, around the reefs and rocks off the coast of Malaysia, Brunei and the Philippines, because ships used to hug those shores to help with navigation and avoid bad weather.
Even if a wreck isn't in a disputed area, tracing its national "ownership" is often complicated. A ship, its owner, its cargo and its crew all may have originated in different countries.
Internationally, the trend in recent years has been toward acknowledging "common heritage," pursuing joint excavation and sharing results among academics from different nations. A 2001 Unesco convention on underwater cultural heritage encouraged states to cooperate when they had a shared interest in a site, but offered no guidance on jurisdiction and no mechanism for dealing with sites in disputed areas.
"If there's a disputed site, what we recommend is just get together and don't get into a fight over it," says Ulrike Guerin, who oversees protection of underwater cultural heritage at Unesco, the United Nations Educational, Scientific and Cultural Organization. "If you look around the world now, the majority of projects are multinational ones."
None of the countries involved in the South China Sea disputes have ratified the Unesco convention. Only China has the resources to enforce its claims to wrecks in the area and to excavate them.
China did little to enforce those claims until March 2012, when the government announced its first-ever crackdown on illegal salvage and archaeological work in China's territorial waters.
The incident at the Scarborough Shoal occurred less than a month later.
China says the standoff stemmed from an incident that April when a Philippines navy ship detained some Chinese fishermen near the Scarborough Shoal. But Chinese officials also have made it clear they regarded Mr. Goddio's project as illegal.
The Chinese marine-surveillance ship that approached the archaeologists was one of three Chinese vessels that took turns monitoring them over the next week or so, according to two people on board the archaeologists' ship and accounts in Chinese state media.
A Philippines coast guard ship was sent to the area but kept its distance. A tense standoff ensued as Chinese and Filipino officials accused one another of violating territorial boundaries.
Eventually, on April 18, the archaeologists' ship was forced to leave, prompting a formal protest from the Philippines' government. China has had effective control of the area since then.
The team abandoned its project. Mr. Goddio declined to comment.
Neither he nor the National Museum of the Philippines has a track record of using finds to justify territorial or ownership claims. "We don't really care who owns the ship," says Sheldon Clyde B. Jago-on, the head of underwater archaeology at the National Museum of the Philippines. "It's our shared heritage. It should be about collaboration. We care about the trade patterns, the trade routes, the cargo, the boat building."
Some experts say the overlap between politics and archaeology is neither surprising nor unique to China. Vietnam is expanding investment in its state-run archaeological program, and this year its Institute of Archaeology opened an underwater-archaeology department.
One of Vietnam's first projects has obvious political resonance—excavation of the site of a naval battle in which Vietnamese forces defeated a Chinese army in 938 A.D., bringing an end to centuries of Chinese rule over Vietnam. That site is on a river inside Vietnam.
The Scarborough Shoal incident, by contrast, marked the first time a country in the region used force to stop another nation's underwater archaeological project, experts say.
"China has the largest navy and the ability to chase people off, and then follow up with archaeological work," says Mark Staniforth, a marine archaeologist at Australia's Monash University who is working with Vietnam's Institute of Archaeology. "There's no sense they want to cooperate or collaborate with anyone."
Write to Jeremy Page at jeremy.page@wsj.com