The nuclear powered USS John C Stennis, as well as its escort ships, were prevented from docking on Friday.
The US said it expected that a separate port visit for another US ship, the USS Blue Ridge, would continue as normal.
A dispute over China's military presence in the South China sea has dogged relations between the US and China in recent years.
The request for the visit was recently denied despite a "long track record of successful port visits to Hong Kong", Pentagon spokesman Bill Urban told Reuters.
The USS Blue Ridge had entered Hong Kong earlier on Friday morning, Reuters reported.
No official reason has yet been given for the denial of permission to the aircraft carrier.
The ship has been touring the Western Pacific region for several months.
Earlier this month the US Defence Secretary, Ash Carter, landed on board the USS John C Stennis to state his support for allies in the region.
"What's new is not an American carrier in this region," he said on 15 April. "What's new is the context of tension which exists, which we want to reduce."
Earlier this month the US and the Philippines agreed to conduct joint patrols in the South China Sea.
China claims most of the sea as its own and has become increasingly assertive.
Contested South China Sea
China has denied a US aircraft carrier permission to make a port visit to Hong Kong, the US state department says.