Sunday's FONOP was the latest in a series of recent moves by the US military in the South China Sea and in the diplomatic arena amid rising tensions between Washington and Beijing.
The USS Decatur was conducting "freedom of navigation" operations on Sunday when it passed 12 nautical miles off reefs in the disputed Spratly Islands.
"The United States has repeatedly sent military ships to South China Sea islands and its adjacent waters, threatened China's sovereignty and security, seriously damaged the relations between the two countries and militaries, and endangered regional peace and stability", Senior Col. Wu Qian, a spokesman for China's Ministry of National Defense, said in a statement.
Gaven Reef is located in the Spratly Islands chain in the South China Sea where China claims seven man-made islands as its own. A Chinese ship approached the USS Decatur, getting within 45 yards of it.
ABC reports of the encounter state that the PLAN vessel was initially 500 yards from the USS Decatur's port side, but moved ahead of the USA ship to cut across its path coming within 45 yards of the front of the Decatur.
The U.S. Navy routinely undertakes FONOP missions worldwide to challenge excessive territorial claims of global shipping lanes.
China's defense and foreign ministries each released statements Tuesday sharply criticizing the United States, though not disputing details of the US accusations involving the Decatur. "The Chinese army is firmly opposed to this".
The US Navy on Tuesday said that a Chinese warship had sailed closed to American destroyer in an "unsafe and unprofessional" manner in South China Sea.
A USA defense official characterized the close encounter as having been of short duration.
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There was no immediate reaction from China, but a similar United States operation in July, involving the disputed Paracel islands, prompted a furious Beijing to deploy military vessels and fighter jets.
Relations between the USA and China have deteriorated over an escalating trade dispute.
The Chinese armed forces will continue to take all necessary steps to protect the country's sovereignty and security, the ministry said.
President Donald Trump ordered new levies on $200 billion in Chinese imports, and Beijing responded with tariffs on $60 billion in American products, nearing the point of running out of US goods to target. They happen all over the world.
"Our forces will continue to fly, sail and operate anywhere global law allows", he said.
This incident comes amid heightened US-China tensions over a broad range of issues.
"They do not want me or us to win because I am the first president ever to challenge China on trade", Trump said.
She said that such USA moves are against the common will of countries in the region and the basic worldwide norms, the state-run Xinhua news agency reported on Tuesday.