Beijing has apparently installed anti-ship cruise missiles and surface-to-air missile systems on three of its outposts in the disputed region, according to USA intelligence reports.
According to sources, the missile system was deployed on several artificial Islands, built by the Chinese in the disputed Spratly archipelago.
She said the administration has brought its concerns "directly" to the Chinese government, and also stated that China will face "near term and long term consequences" for the missile installations.
In March, the military began their annual spring air force drills in the South China Sea, involving the use of powerful military aircraft such as H-6K bombers, Su-30, and Su-35 fighters.
It claims an enormous swath of territory through the centre of the South China sea based on its self-proclaimed principle of nine dash line and has attempted to reinforce its hold on the area by creating and militarizing artificial islands in the Spratlys and the Paracels.
"We will continue to do our operations", she said.
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The Philippines' presidential palace said it did not have confirmed reports on the missile deployment.
Even with China continually on edge, the US has reaffirmed that it will continue to not only keep a noticeable presence, but also conduct drills as needed.
"China, of course, has a unique responsibility as a permanent member of the Security Council, to uphold peace and security around the world".
The construction of hangars on Mischief Reef is said to be part of China's militarization of the West Philippine Sea.
The US Navy has frequently sent warships and aircraft carriers to patrol the South China Sea area.
Last month China's military issued "robust" challenges to three Australian warships as they travelled through the South China Sea to Vietnam.
The YJ-12B anti-ship cruise missiles are capable of engaging surface vessels within 295 nautical miles of the reefs, while the HQ-9B surface-to-air missiles have a range of 160 nautical miles, CNBC reported.