The US Navy says Chinese approval for its vessels to enter Hong Kong for the Thanksgiving holiday has come too late.
The USS Kitty Hawk, based in Japan, will be decommissioned in 2008
The navy said the ships had already left the area, after China initially refused their request to dock.
China later said it would allow the flotilla to dock in the harbour for "humanitarian" reasons.
About 8,000 personnel on the USS Kitty Hawk and other vessels had expected to go ashore, but instead have spent most of Thanksgiving on the South China Sea.
When the approval to dock was given, the US ships had already left port to return to their base in Japan.
Chinese foreign ministry spokesman Liu Jianchao confirmed the apparent U-turn in policy, saying China had informed the US of its decision.
"We have decided to allow the Kitty Hawk strike group to stay in Hong Kong during Thanksgiving, and it is a decision out of humanitarian consideration only," Mr Liu said.
Families of many of the crew members had flown out to Hong Kong to spend the holiday with their loved ones.
Earlier, US consular officials said they had been in touch with the families to explain the situation.
"For a lot of guys, this is their favourite port in the entire area of operations for us in the Western Pacific," a crew member told Reuters news agency before China's decision to allow them entry was known.
"This is also the Kitty Hawk's last port visit here before being decommissioned - so it was a big deal."
Hong Kong has long been a favoured port of call for the US military, but Beijing's approval has been required since 1997, when the UK handed the territory back to China.
The Kitty Hawk, which is based in Japan, is the US Navy's oldest active ship and is due to be decommissioned next year.