Sources told CNBC that they were deployed within the past 30 days - marking the first time that missiles had ever been installed in the Spratlys.
The Chinese authorities have secretly transferred the disputed Spratly Islands in the South China sea and anti-ship missiles and air defense systems.
"There will be near-term and long-term consequences, and we'll certainly keep you up to date", she added.
China has defended the installation of the missiles, saying they are "necessary national defence facilities", CNN reports.
"The relevant deployment targets no one. And it's in their interest to ensure that there's a free navigation of worldwide waters", she said.
A U.S. official said said that in a few instances, military grade lasers from the Chinese base had been pointed at aircraft.
Beijing claims an enormous swath of territory through the center of the sea, and has attempted to reinforce its hold on the area by creating and militarizing artificial islands in the Spratlys and the Paracels. Dispute the controversy, China has been carrying land-reclamation efforts, building artificial reefs and has established air bases, radar and communication systems, naval facilities and defensive weaponry.
"Any action to militarize unilaterally features in the South China Sea would go against that responsibility and that role".
Earlier, the USA lodged a formal complaint with Beijing after Chinese nationals pointed lasers at United States military aircraft near a base in Djibouti in a number of incidents in recent weeks.
The White House has warned China that it will not accept the continued military build-up in the hotly contested region.
The same month, Australian warships en route to Vietnam were challenged by the Chinese navy as they traversed the South China Sea, leading Prime Minister Malcolm Turnbull to assert Australia's right to travel global waters.
Asked about the report, White House spokeswoman Sarah Sanders said there would be consequences but not what they would be.
Last month China's military issued "robust" challenges to three Australian warships as they travelled through the South China Sea to Vietnam.