The US military conducted "freedom of navigation" operations against 13 countries including India last year, including several to challenge China's claims in the South and East China seas, according to an annual Pentagon report released on Monday.
The report were against India, China, Indonesia, Iran, Malaysia, Libya, The Maldives, Oman, The Philippines and Vietnam.
The freedom of navigation operations involve sending US Navy ships and military aircraft into areas where other countries have tried to limit access. The aim is to demonstrate that the international community does not accept such restrictions.
A US guided-missile destroyer conducted a freedom of navigation patrol near one of China's man-made islands in the Spratly archipelago in October. US military flights near the islands have been warned off.
US defense secretary Ash Carter said the Navy would continue to operate in the region despite China's condemnation of the patrols.
China's defense ministry said in a statement on its website late on Monday that it was deeply concerned by such operations.
"The United States carries out militarization in the South China Sea in the name of freedom of navigation and overflight, threatens coastal nations' sovereignty and security and destroys regional peace and stability," the ministry said.
It made the comment in response to what it said were reports of recent U.S. military flights near Scarborough Shoal - known by Beijing as Huangyan Island - an area China seized control of after a stand-off with the Philippine coast guard in 2012.
Admiral Harry Harris, the head of US Pacific Command, said this year the Navy would step up the freedom of navigation operations in the South China Sea because of concerns China is attempting to assert its dominance by building military facilities there.
U.S. freedom of navigation operations last year also challenged China's claims of jurisdiction in the airspace above its maritime Exclusive Economic Zone as well as restrictions it has tried to impose on aircraft flying through an Air Defense Identification Zone over the East China Sea.