The US Indo-Pacific Command said its pilot was forced to swerve when the Chinese Navy J-11 jet flew within six metres of its RC-135 plane on December 21.
The US plane was “lawfully conducting routine operations over the South China Sea in international airspace”, it said in a statement. The pilot was forced to “take evasive manoeuvres to avoid a collision".
China claims the whole of the strategically important South China Sea but other countries including Brunei, Taiwan and Vietnam also claim parts of it as their own territory.
“The US Indo-Pacific Joint Force is dedicated to a free and open Indo-Pacific region and will continue to fly, sail and operate at sea and in international airspace with due regard for the safety of all vessels and aircraft under international law," the statement said.
“We expect all countries in the Indo-Pacific region to use international airspace safely and in accordance with international law," it said.
China regularly demands US ships and planes leave the area. The US says it is fully entitled to operate in and over the South China Sea and ignores the Chinese demands.
In 2001, an in-air collision between a Chinese jet and a US jet in the area killed the Chinese pilot and caused the plane to go missing.
Chinese Foreign Ministry spokesperson Wang Wenbin accused the US of posing "serious threats to China’s national security", with its surveillance operations in a daily briefing on Friday. He did not provide further details.
“China will continue to take necessary measures to firmly defend its sovereignty and security and work with regional countries to firmly defend the peace and stability of the South China Sea," Mr Wang said at a daily briefing on Friday.
Mr Wang also renewed Beijing’s objections to US arms sales to Taiwan, the self-governing island democracy that Beijing threatens to bring under its control by force if necessary.
The US this week approved the sale of a $180m (£149 million) anti-tank system to Taiwan as the threat from China’s military rises.
The US has no formal ties with Taiwan but is required by US law to ensure the island has the means to defend itself.