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 (ASEAN) 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.
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 territorial claims. Vietnam, Malaysia, Brunei, the Philippines and Taiwan have rival claims on the area.
At the end of the ASEAN summit in Washington D.C. on Tuesday, President Barack Obama reaffirmed the United States' "strong commitment to a regional order where international rules, norms, and the rights of all nations --large and small-- are upheld."
He said that countries at the summit discussed the need to take "tangible steps in the South China Sea to lower tensions, including a halt to further reclamation, construction and militarization of the disputed areas."
"I reiterate that the United States will continue to fly, sail and operate wherever international law allows, and we will support the right of all countries to do the same," Obama said.
The United States has said that it will continue conducting "freedom of navigation patrols" by ships and aircraft through the South China Sea. China has repeatedly called these patrols, which encroach on waters China claims ownership of, provocative and warned that they risked military action in response.
Ernest Bower, senior adviser and Sumitro Chair for Southeast Asia studies at the Center for Strategic and International Studies (CSIS), told CNBC that the U.S. was not asking ASEAN to choose between it and China, but rather to "strengthen themselves and become a solid core for new regional security and economic architecture."
"The genius of ASEAN is it doesn't have a sovereign identity and because of that, it doesn't have a sort of national interest like the U.S. or China does," Bower said.