The islands, thought to hold potentially significant oil and gas reserves, are claimed by China, Taiwan, Malaysia, Brunei, the Philippines and Vietnam.
"We are deeply concerned about the US remarks. The US side must clarify this," Hua Chunying said at a daily press conference in Beijing.
The latest tensions between China and the United States have emerged ahead of State Secretary John Kerry's visit to Beijing scheduled for May 16-17. Acting State Department spokeswoman Marie Harf said Kerry will meet senior Chinese government officials "to advance US priorities" ahead of this June's US-China Strategic and Economic Dialogue (S&ED).
Hua, meanwhile, affirmed China's intent to safeguard its territorial sovereignty despite stressing its adherence to the principle of freedom of navigation.
"The freedom definitely does not mean that foreign military vessels and aircraft can enter one country's territorial waters and airspace at will," the spokeswoman said.