The Ministry of National Defence expressed its opposition to frequent and close-in US reconnaissance of China on Monday.
The comments followed a top US navy admiral's joining a seven-hour-long surveillance flight over the South China Sea over the weekend.
US aircraft have conducted frequent reconnaissance flights near China for some time, which has gravely undermined Sino-US trust and China's security interests, and is highly likely to cause maritime and airborne incidents, the ministry's press office said.
The ministry commented to China Daily after the US Pacific Fleet said its new fleet commander, Admiral Scott Swift, joined the surveillance mission on board a P-8A Poseidon plane on Saturday.
The US did not give any specific details, including which parts of the sea it flew over, saying only that it was a routine flight to witness the full range of capabilities of the aircraft, a new multipurpose spy plane.
Peace and stability in the Asia-Pacific region is in all parties' interests, the ministry said, urging the US to make more efforts to maintain it, and keep its promise not to take sides in South China Sea issues .
Fan Jishe, a US studies researcher at the Chinese Academy of Social Sciences, said the flights are one of the high-profile moves by the US recently to support Asian allies that have regional maritime claims that overlap those of China.
The moves are also an attempt to put pressure on China after Beijing said the country has completed land reclamation on some islands and reefs in the Nansha Islands, Fan said.
In May, Beijing described a US P-8 surveillance flight carrying a CNN team over the South China Sea as "irresponsible and dangerous". As for the latest flight, the US Pacific Fleet released photographs of Swift on board the plane over the sea on Sunday.
Fan said these moves, part of Swift's recent visit to the Philippines, are likely to send an incorrect message to US allies and encourage them to exaggerate the US security commitment. "This won't help to ease the maritime tension but will aggravate problems instead," he said.
Philippines Defence Secretary Voltaire Gazmin welcomed the flight with Swift, saying it showed the US commitment to come to the aid of allies that have territorial disputes with China.
Earlier this month, Manila argued its case before a UN-backed tribunal, challenging China's claim over the sea. China has opposed any move by the Philippines to initiate and push forward the proceeding.
Mo Jingxi and The Associated Press contributed to this story.