"China is very displeased with this and will bring up the issue with the United States side", the ministry added.
The official said the interactions were all "safe and professional", with the operation lasting about six hours.
China claims almost all of the sea, through which $5 trillion in annual shipping trade passes and which is believed to sit atop vast oil and gas deposits. Tensions are mounting. This is a gradual process, and the problem is that the South China Sea is now becoming a geopolitical whirlpool sucking in more and more countries.
For the Pentagon and the American security establishment, China stands at a critical stage where it could translate its massive economic might into modern military technology and political muscle in a matter of years, rather than decades.
U.S. Secretary of State Rex Tillerson, Australian Foreign Minister Julie Bishop and Japan's Taro¯ Ko¯no, also called on ASEAN foreign ministers to swiftly negotiate a legally binding code of conduct with China aimed at preventing an escalation of conflicts in the West Philippine Sea, one of the world's busiest waterways.
The US has maintained that the South China Sea is worldwide water, and that sovereignty in the area should be determined by the UNCLOS.
"China is very displeased with this and will bring up the issue with the USA side", the ministry said in a statement.
A dispute over the Senkaku Islands in the East China Sea continues to boil between the two Asian giants.
"That is true in the South China Sea as in other places around the globe". This is partly because not all 10 members are claimants to the South China Sea. It found no evidence that China had historically exercised exclusive control over the waters or resources within the Nine-Dash Line.
China is expanding artificial islands in disputed South China Sea areas despite saying it stopped two years ago, according to a security think tank that released satellite images it said showed the land reclamation. The ministers also reaffirmed the need to "pursue peaceful resolution of disputes in accordance with worldwide law including the 1982 United Nations Convention on the Law of Sea".
However, if the U.S Navy encroaches upon Chinese maritime territory, "we will not tolerate such behavior", he added. The reef is part of a string of highly strategic islets and shoals where Beijing has built artificial islands to stage military bases.
The official spoke on condition of anonymity because the official was not authorized to speak to the press about the matter. "If China helps us, I feel a lot differently toward trade", he said.
The Association of Southeast Asian Nations (ASEAN) and China should establish a set of rules that is "legally binding, meaningful, effective and consistent with global law", the three foreign ministers said.
He also insisted that such operations "seriously endanger lives".
Beijing protested on Friday, the official Xinhua news agency reported.