The US says the Impeccable was conducting routine manoeuvres
China says a US Navy ship involved in Sunday's confrontation with its vessels off the southern island of Hainan violated international and Chinese law.
Foreign ministry spokesman Ma Zhaoxu said US complaints that five Chinese vessels had harassed the USNS Impeccable were "totally inaccurate".
Beijing says the ship was conducting activities within the waters of its exclusive economic zone.
The US earlier complained to China's military attache over the incident.
It said the Chinese ships manoeuvred dangerously close to an unarmed US navy surveillance vessel while it 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", a Pentagon statement said.
The Pentagon identified the Chinese boats as a naval intelligence-gathering ship, a Bureau of Maritime Fisheries Patrol Vessel, a State Oceanographic Administration patrol vessel, and two small trawlers.
Sunday's incident followed days of "increasingly aggressive" acts by Chinese ships, US officials said.
'Confusing black and white'
China called the US complaints unacceptable.
SOUTH CHINA SEA TENSIONS
Territorial claims from China, the Philippines, Taiwan, Brunei, Vietnam and Malaysia overlap in resource-rich sea
Hosts some of the world's busiest shipping lanes
China says the US was in its Exclusive Economic Zone - but the two sides disagree on what activities are allowed in an EEZ
"The US Navy ship Impeccable broke international law and Chinese laws and regulations," Mr Ma said.
"The US claims are gravely in contravention of the facts and confuse black and white," he added.
China views most of the South China Sea as its territory - but the Philippines, Vietnam, Malaysia, Brunei and Taiwan also lay claim to islands there.
Under international law, Chinese territorial waters extend 12 nautical miles (22km) off its coast and its Exclusive Economic Zone (EEZ) extends 200 nautical miles.
China says that any intelligence data gathering by foreign governments within its EEZ is illegal - but the US does not agree with this.
The Impeccable is used to map the ocean floor with sonar. The information is used by the US navy to steer its own submarines or track those of other nations.
There is a large Chinese submarine base on Hainan island.
Aggressive manoeuvring by ships of rival navies in sensitive international waters is not uncommon, correspondents say.
But Washington was sufficiently disturbed by the incident involving the Impeccable to make its concerns public.