Taiwan defense ministry spokesman Major General David Lo told Reuters the missile batteries had been set up on Woody Island. The island is part of the Paracels chain, under Chinese control for more than 40 year but also claimed by Taiwan and Vietnam.
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"Interested parties should work together to maintain peace and stability in the South China Sea region and refrain from taking any unilateral measures that would increase tensions," Lo said on Wednesday.
A US defense official also confirmed the "apparent deployment" of the missiles, first reported by Fox News.
Images from civilian satellite company ImageSat International show two batteries of eight surface-to-air missile launchers as well as a radar system, according to Fox News.
News of the missile deployment came as Obama and leaders of the Association of Southeast Asian Nations concluded a summit in California, where they discussed the need to ease tensions in the region but did not include specific mention of China's assertive pursuit of its claims in the South China Sea.
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China claims most of the South China Sea, through which more than $5 trillion in global trade passes every year, and has been building runways and other infrastructure on artificial islands to bolster its claims.
"We discussed the need for tangible steps in the South China Sea to lower tensions including a halt to further reclamation, new construction and militarization of disputed areas," Obama told a news conference.
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