Beijing's comments follow a formal US complaint to China's military attache at the Pentagon over the incident, which happened on Sunday.
The US said five Chinese ships manoeuvred dangerously close to an unarmed navy surveillance vessel.
A Chinese spokesman said that the claims were "totally unacceptable".
"The US claims are gravely in contravention of the facts and confuse black and white," Foreign Ministry spokesman Ma Zhaoxu told a regular news briefing.
The US said the incident happened as the USNS Impeccable was on routine operations in international waters 75 miles (120km) south of Hainan island.
The ships "aggressively manoeuvred" around the Impeccable "in an apparent co-ordinated effort to harass the US ocean surveillance ship while it was conducting routine operations in international waters", a Pentagon statement said.