The official said all U.S. military operations in the area "are designed in accordance with worldwide law and demonstrate that the United States will fly, sail and operate wherever global law allows".
"U.S. forces operate in the Indo-Pacific region on a daily basis, including the South China Sea".
The freedom of navigation operations "challenge excessive maritime claims and demonstrate our commitment to uphold the rights, freedoms, and uses of the sea and airspace guaranteed to all nations under global law", the official added.
There was no immediate reaction from China, but a similar American operation in July that involved the disputed Paracel islands infuriated Beijing, which deployed military vessels and fighter jets.
The FONOP sailed within 12 nautical miles of Gaven and Johnson reefs through territory claimed by China, the Philippines, Taiwan, and Vietnam, on the eve of China's national day.
Fuel price hike: Petrol prices cross Rs 91 per liter in Mumbai
Meanwhile, the price of subsidised LPG cylinder has been increased from Rs 499.51 to Rs 502.40 (a hike of Rs 2.89). The increase in transportation fuel prices comes amid surging crude oil prices.
But the US has continued to challenge China's policing of those waters.
Earlier this week, the US flew B-52 bombers over the South China Sea and East China Sea, areas considered sensitive by the Chinese military.
The flights drew a protest from Beijing, which labeled them provocative.
"There's nothing out of the ordinary about it, nor about our ship sailing through there", Mattis told reporters at the Pentagon.
The sail-by on Sunday also comes amid heightened tensions between Washington and Beijing over trade and diplomatic issues. Last week, new tariffs targeting $200 billion of Chinese goods came into effect, the latest salvo in President Donald Trump's ongoing trade war with China. "We're just going through one of those periodic points where we've got to learn to manage our differences".