The U.S. Defense Department said on Friday, Censor.NET reports citing Reuters.
A Pentagon spokesman, Commander Bill Urban, said a U.S. warship, the USS Blue Ridge, was currently in Hong Kong on a port visit and the United States expected that to continue.
The Chinese government and its embassy in Washington did not immediately respond to requests for comment.
Urban said the request for the Hong Kong visit by the carrier and its accompanying vessels, which have been patrolling the South China Sea, was recently denied, despite a "long track record of successful port visits to Hong Kong."
The nuclear-powered Stennis has been conducting patrols in the South China Sea, which China claims most of and where Beijing has sparked U.S. and regional concerns by building artificial islands to bolster its claims.
U.S. Defense Secretary Ash Carter visited the Stennis while it transited the South China Sea on April 15 to underscore U.S. concerns about the need to maintain freedom of navigation in the South China Sea in the face of Chinese moves.
A wide range of U.S. military vessels and aircraft have long routinely stopped in Hong Kong, a reflection of the "one country, two systems" formula under which Britain handed the global financial hub back to China in 1997.
The visits occasionally have been suspended in periods of heightened tensions, such as after a mid-air collision between a U.S. EP-3 surveillance plane and a Chinese plane off China's Hainan island in 2001.
The United States has stressed the importance of good relations with China's military to avoid misunderstandings and Chinese military officers are invited routinely aboard U.S. ships during port visits, and are sometimes flown out to land on U.S. carriers at sea.
While there, he dismissed China's characterization of a more robust U.S. military presence in the region as being the cause of heightened tensions. The United States has in turn accused China of militarizing its outposts in the South China Sea by building airstrips and other facilities.