"The United States naval vessels Antietam and Higgins entered without Chinese government permission into territorial waters" around the islands, which China calls the Xisha Islands, Mr Wu said in the statement.
The ministry said late Sunday that the Chinese military had warned the two USA warships to leave after they entered waters near the contested Paracel Islands in the strategic waterway.
At the same time, US Defense Department spokesman Christopher Logan has firmly denied Beijing's accusations of the US violating Chinese sovereignty in the disputed South China Sea, underlining that US Navy operates in the area in accordance with global law.
Chiefs from the Pentagon have continuously accused China of building up it military power in the South China Sea to gain control of oil and gas rich region.
'We conduct routine and regular Freedom of Navigation Operations (FONOPs), as we have done in the past and will continue to do in the future, ' US Pacific Fleet said in a statement. It also came just days after the Pentagon uninvited China from a major USA -hosted naval drill.
These types of operations are known as "freedom of navigation" with naysayers claiming that they have little impact on Chinese behavior and are largely symbolic.
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Beijing says aircraft carriers are needed to protect its coastline and trade routes, although they are also seen as backing up Beijing's claims to self-governing Taiwan and the South China Sea.
Earlier in the month, the U.S. also formally protested against the deployment of missiles and radar equipment on three artificial islands China has built in the Spratly islands. China has refused to acknowledge the arbitral ruling and continues to claim the South China Sea in its entirety.
Philippines President Rodrigo Duterte has said China will cross a red line if it unilaterally mines the natural resources of the South China Sea, according to the country's Foreign Minister Alan Peter Cayetano.
Last week China showed off the completion of an airstrip by flying bombers and other planes to the island base. Recent Chinese actions on areas within the country's EEZ include the reported presence of two Chinese military planes on Panganiban or Mischief Reef, and China's unveiling of a monument to mark its construction work in Kagitingan or Fiery Cross Reef.
'It's also a decision taken lightly and is unhelpful to mutual understanding between China and the US, ' Wang said at a press conference with Secretary of State Mike Pompeo after the two met in Washington.
The decision to pull China's invitation comes amid new tensions between Beijing and Washington.