The Chinese side immediately conducted verification and identification on the US ships and warned them to leave, said the spokeswoman.
The US is "determined to stir up trouble in the South China Sea, create tension and undermine peace", Hua said.
But Hua slammed the USA, arguing that "China has indisputable sovereignty over islands in the South China Sea, including the Second Thomas Shoal, Mischief Reef, and the adjacent waters".
They will try to reach a trade deal before a March 1 deadline after which the U.S. has threatened to increase tariffs on US$200 billion worth of Chinese imports and risk retaliatory action from China.
China says the bases are essential for self-defense and accused the USA of ramping up tensions in the region by sending battleships and warplanes close to the disputed islands.
'China has indisputable sovereignty over islands in the South China Sea, including the Second Thomas Shoal, Mischief Reef, and the adjacent waters, ' Hua said.
"The relevant actions of the United States warships violated Chinese sovereignty, and undermined peace, security, and order in the relevant sea areas", Hua said.
A spokesperson for the U.S. Navy's 7th Fleet confirmed the FONOP Monday afternoon with global media, stating that the operation was conducted "to challenge excessive maritime claims and preserve access to the waterways as governed by worldwide law". The deployment is seen as the latest attempt by Washington to stand up to what it believes are attempts by Beijing to limit freedom of navigation in the strategic waters, where Chinese, Japanese and other Southeast Asian navies operate.
Other regional nations-such as the Philippines and Vietnam-lay claim to part of the waterway and the US routinely pushes back against China by sending ships to patrol the sea. The two countries have traded barbs over what United States said was Beijing's military installation building on artificial islands and reefs.
China claims nearly all of the strategic South China Sea and frequently lambasts the USA and its allies over naval operations near Chinese-occupied islands.
Top US officials have attacked China for everything from human rights abuses to cyber espionage in America.
The US and its allies periodically send planes and warships near South China Sea islands and reefs claimed by Beijing to signal their right under worldwide law to pass through the waters, invariably angering China.
The two countries are also at loggerheads over regional security, with the U.S. offering support to the island nation of Taiwan, which China also claims as its own.