Tensions have been growing across multiple fronts, from the Trump administration's tariffs on Chinese goods to new sanctions announced against the Chinese military.
The destroyer lance-missile USS Decatur was Sunday, what the u.s. military calls "operation for freedom of navigation" when it happened less than 12 nautical miles from reefs Gaven and Johnson, in the archipelago of the Spratleys.
"The U.S. side repeatedly sends military ships without permission into seas close to South China Seas islands, seriously threatening China's sovereignty and security, seriously damaging Sino-U.S. military ties and seriously harming regional peace and stability", the ministry said.
Tensions have flared yet again in the South China Sea where a Chinese destroyer almost collided with an American warship while attempting to force the USA vessel to leave the disputed area which it claims as its own.
The U.S. regularly conducts FONOPS, or freedom of navigation operations, in disputed seas around the world to challenge "excessive" maritime claims.
US Pacific Fleet spokesman Lt Cmdr Tim Gorman said the Chinese warship approached the USS Decatur in an "unsafe and unprofessional manoeuvre" on Sunday near Gaven Reefs in the South China Sea.
US warships often maneuver in close formation, but their movements are closely coordinated, following standardized and procedures and principles, and the maneuvering ships rarely have less than 1,000 yards between them.
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"In response, the Chinese navy identified and warned the ship to leave in accordance with [the] law", said the MoFA without speaking of an "unsafe" encounter with the U.S. destroyer. The People's Liberation Army has sought to contest such moves in territory it considers China's.
"As we have for decades, our forces will continue to fly, sail and operate anywhere global law allows".
The Chinese manoeuvre nearly caused a collision, United States official said. Since then, China has engaged in numerous unsafe incidents against usa surveillance planes, while generally downplaying the danger they posed afterwards.
Tuesday's statement, unusual in clearly announcing the run-in with the Chinese vessel, reaffirmed that the USA would not halt its operations in the area.
The US Secretary of Defense James Mattis reportedly pulled out of his planned visit to Beijing in October where he was slated to discuss security issues with senior Chinese officials.
Relations between the US and China have deteriorated over an escalating trade dispute.
China recently denied a US request for the Navy's USS Wasp to make a port call in Hong Kong in October.