Tensions between the two economic superpowers have risen in recent years over the disputed waterway, which China claims almost in full despite counter-claims from other Asian nations.
Chinese J-10 warplanes intercepted a US Navy P-3 that was operating in international airspace Wednesday, according to Pentagon spokesman Commander Gary Ross.
The US deemed the move "unsafe and unprofessional" and pledged to convey its concerns to the Chinese government.
But the Chinese defence ministry on Sunday said the Pentagon's account of the incident "was not in accordance with the facts".
"On May 25, a US patrol plane carried out reconnaissance activities in the airspace southeast of Hong Kong, China," it said in a statement on its website.
"The Chinese military aircraft carried out identification in accordance with law. The operations were professional and safe."
Beijing also accused Washington of trespassing last week after it sailed a warship near a reef claimed by Beijing in the South China Sea -- the "first freedom of navigation" exercise under US President Donald Trump.
These actions "infringed on our sovereignty and security, endangering the safety of front-line personnel of both sides," the defence ministry said in the statement.
"The behaviour is the root cause of the military security problems in maritime and sky areas between US and China.
"China's armed forces will resolutely perform their duties and resolutely safeguard our sovereignty and security," it added.
Beijing has rapidly built up reefs in the South China Sea into artificial islands capable of hosting military planes.
The United States has challenged the annexation of these islets and advocated a diplomatic settlement to disputes, arguing that Beijing's actions threaten freedom of navigation and overflight.
The tensions come ahead of a major regional security summit in Singapore this week.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)