"The US has denied its involvement in the ongoing violent incidents in Hong Kong on many occasions", said ministry spokeswoman Hua Chunying.
"The U.S. Navy has a long track record of successful port visits to Hong Kong and we expect them to continue".
Demonstrators say they are fighting the erosion of the "one country, two systems" arrangement that enshrined some autonomy for Hong Kong after China took it back from Britain in 1997.
"The primary goal would be to intimidate Hong Kong protesters by suggesting they might move in and restore "stability" by force", said Mr Andrew Chubb, a Chinese politics and foreign policy researcher at Lancaster University.
Hong Kong airline Cathay Pacific said in a statement it had canceled 272 flights over the last two days, affecting more than 55,000 passengers, while 622 departures and arrivals went ahead.
Hong Kong leader Carrie Lam said on Tuesday the city had been pushed into a state of "panic and chaos".
The protesters had staged continuous sit-ins at the airport over the weekend to put pressure on the government to accede to "five demands", including the complete formal withdrawal of a proposed extradition bill that ignited the initial protests months previous.
Protesters physically blocked travellers from accessing flights throughout the afternoon, before battling with riot police outside the terminal later that evening and turning on two people they accused of being spies or undercover police.
The Chinese city of Shenzen is located across the border from Hong Kong. One of the men turned out to be a reporter for the Communist Party-owned newspaper Global Times. "He has no other task except for reporting".
By early Wednesday, most protesters had left and many flights were operating as scheduled in the morning.
U.S. President Donald Trump said on Twitter overnight the Chinese government was moving troops to the border with Hong Kong and urged calm.
The violence came after Hong Kong's Airport Authority announced that all check-in services would be suspended for another night, due to terminal operations being "seriously disrupted". A Chinese official with the agency overseeing the city used "terrorism" to describe the protests, invoking a term used to justify sending in forces to repress minority Muslims in the far west region of Xinjiang.
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