US Pacific Fleet deputy spokesman Nate Christensen said the Chinese destroyer had "approached USS Decatur in an unsafe and unprofessional manoeuvre in the vicinity of Gaven Reef in the South China Sea".
A Chinese destroyer sent to escort the USS Decatur on a "freedom of navigation" sail-by in the disputed South China Sea has come dangerously close and forced the US vessel to maneuver to "prevent collision", the US Navy said.
The Chinese "destroyer approached within 45 yards (meters) of Decatur's bow, after which Decatur maneuvered to prevent a collision".
"On September 30, without permission of the Chinese government, the USA destroyer Decatur entered neighbouring waters of islands and reefs of China's Nansha Islands", Chinese foreign ministry spokesperson Hua Chunying said in a statement on Tuesday.
The 12-mile distance is commonly accepted as constituting the territorial waters of a landmass.
"The PRC destroyer conducted a series of increasingly aggressive maneuvers accompanied by warnings for [the] Decatur to depart the area", Lt. Cmdr.
The missile destroyer USS Decatur (pictured in 2016) operates in the South China Sea. -China tensions over a broad range of issues.
US Air Force B-52 Stratofortress heavy long-range bombers flew through both the East and South China Sea last week.
While the Navy conducts such freedom of navigation operations all over the world, China is particularly sensitive about the operations when they come near areas where the Chinese government has built islands and established military facilities on disputed maritime features.
It added: "China's military is resolutely opposed to this".
The presence of American ships near the Chinese-claimed archipelago off the coast of the Philippines, Malaysia and southern Vietnam is "seriously threatening China's sovereignty and security" and "seriously undermining the relations between the two countries and the two militaries", Wu added.
China's Foreign Ministry said in a separate statement it strongly urged the United States to stop such "provocative" actions and to "immediately correct its mistakes".
Although the US takes no position on the competing claims, its navy regularly carries out freedom of navigation operations - known as "FONOPs" - by sending warships and aircraft near disputed waters to demonstrate the right to travel through what it considers global waters and airspace.
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 Chinese military resolutely opposes such actions", he said, adding that China respects and safeguards the freedom of navigation and overflight in the SCS in accordance with global law, but resolutely opposes any illegal provocation in the name of 'freedom of navigation.' "The Chinese military will fulfil its defence duty and continue to take all necessary measures to firmly safeguard the sovereignty and security of the country, as well as the regional peace and stability", he said.
Last week, the Pentagon said the B-52s had transited over the South China Sea as part of "regularly scheduled operations created to enhance our interoperability with our partners and allies in the region".
China reportedly cancelled the security meeting with Mattis that had been planned for October.