The two US bombers on December 10 flew into the airspace near an island and reef of Nansha Islands (Spratly islands) claimed by China and Vietnam.
Military personnel on the island and reef went on high alert and warned the aircraft to leave, the Chinese Defence Ministry said in a statement.
"In the morning of 10 December, two US B-52 bombers entered air space over the Chinese Nansha islands and nearby areas without authorisation," the statement said.
China claims whole of the South China Sea (SCS). Beijing's claim, however, is strongly contested by the Philippines, Vietnam, Malaysia, Brunei and Taiwan.
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For its part, the US asserts that it do not recognise China's claims over the SCS.
China claims that the whole of the SCS is its part of it from ancient times. China vehemently protested in October when a US warship sailed through the waters near an artificial island being built by it disregarding protests from the Philippines and other maritime claimants.
The Chinese Defence Ministry said the US has continuously sent military ships and planes as a show of force and created tensions in the waters and airspace.
Such actions have severely threatened the safety of Chinese personnel and facilities as well as peace and stability of the region, it said.
The ministry demanded that the US immediately adopt measures to avoid such dangerous actions in order to prevent damaging relations between the two militaries and countries.
Meanwhile, the Pentagon said the B-2 bombers flying within two nautical miles of the artificial island build by the Chinese in South China Sea was unintentional and has ordered an investigation into it.
"For this mission, there was no intention of flying to within 12 nautical miles," Pentagon spokesman Cmdr. Bill Urban said.
"The Chinese have raised concerns with us about the flight path of a recent mission. We are looking into the matter," Urban said.