Foreign Ministry spokeswoman Hua Chunying warned the US against "hyping up militarization and stirring up trouble," while promising that China would take all necessary measures to defend its sovereignty.
"US doing whatever they want is risky and China will not be threatened by any military warships," Mr Hua told reporters at a daily briefing in Beijing.
This week's flyby near Scarborough Shoal, which China took from the Philippines in 2012, came after US Defence Secretary Jim Mattis accused Beijing of "intimidation and coercion" in the South China Sea.
China claims almost the entirety of the sea - resource-rich waters that include some of the world's busiest shipping lanes - despite overlapping claims from neighbours including the Philippines, Vietnam and Taiwan.
Speaking at a summit of top security officials in Singapore last weekend, Mattis said China has deployed anti-ship missiles and surface-to-air missiles and landed nuclear capable bombers on the disputed islands. He vowed that the Indo-Pacific would remain a "priority theatre" for US forces.
That naval confrontation came shortly after the Pentagon withdrew its invitation for China to participate in multinational naval exercises near Hawaii to protest China's military moves in the South China Sea.
Despite rising tensions, Mr Mattis is expected to visit Beijing at an unannounced date. He said last weekend he would travel soon on China's invitation.
China's Defense Ministry has said it would welcome Mr Mattis and hoped for continued exchanges with the US military.
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