The rare refusal to allow the aircraft carrier John C. Stennis, and several other vessels accompanying it, to visit the port comes two weeks after the Stennis hosted the defense secretary, Ashton B. Carter, on a visit to the South China Sea, where the United States is challenging what it sees as excessive maritime claims by China.

During the trip, Mr. Carter criticized the Chinese and said the United States would work with its allies in the region.

"America's policy continues to be one valued on principles of peaceful resolutions of disputes, lawful settlement of things like territorial disputes like the South China Sea, or anywhere else, freedom of navigation, freedom of commerce," Mr. Carter said at the time.