Beijing, meanwhile, went ahead with plans for a high-profile port call of its own, making the Chinese military's first visit to Japan since World War II.
So, on Friday, a Chinese destroyer and the aging American aircraft carrier sat docked in the same waters, at separate ports, one quietly awaiting two months of repairs and the other basking in a flurry of welcoming ceremonies, honor bands and smiling assurances that China's ever-growing military is "very transparent."
Officially, Tokyo hailed the Chinese ship's visit.
"This is truly a new page in Japan-China relations," Adm. Eiji Yoshikawa, the chief of staff for Japan's navy, said at a ceremony for the guided missile cruiser Shenzhen, which docked at a Tokyo pier on Wednesday. "We welcome this visit with all our hearts."
But both Tokyo and Washington are deeply concerned about recent Chinese military activities, particularly its rapid improvements in missile technology, the modernization of its huge standing army and the expanding reach of its navy.
Early this year, tensions came to a head when China used a ground-based missile to shoot down an old weather satellite at an orbital height similar to that used by the U.S. military. It was the first-ever such test by any nation.
Tokyo and Washington are also troubled by double-digit growth in China's annual military spending, coupled with Beijing's reluctance to divulge military-related information, all of which made the Kitty Hawk incident last week even more disconcerting.
Relations between the U.S. and China have also been strained in recent months by disputes over trade and Iran's nuclear program.
Several days before the aircraft carrier and its strike group were turned back, Beijing refused to let two U.S. Navy minesweepers enter Hong Kong harbor to escape an approaching storm and refuel. The minesweepers, the Patriot and the Guardian, were instead refueled at sea and returned safely to their home port in Japan.
U.S. military officials protested Beijing's seeming caprice. President Bush mentioned it in a meeting with Chinese Foreign Minister Yang Jiechi at the White House on Wednesday.
Yang called it a "misunderstanding," but offered no apology.
But in Beijing, Foreign Ministry spokesman Liu Jianchao later backed away from that characterization, saying that ties had been "disturbed and harmed" by "erroneous" U.S. actions.
Liu specifically mentioned the U.S. Congress' awarding its highest civilian honor to the Dalai Lama last month as an issue that had upset relations. Though the Tibetan spiritual leader is lauded in much of the world as a figure of moral authority, Beijing demonizes the monk and claims he seeks to destroy China's sovereignty by pushing for independence for Tibet.
Also hurting relations were arms sales to Taiwan, an island which China regards as a renegade province, he said.
But U.S. military officials balked at such explanations.
"As someone who has been going to sea all my life, if there is one tenet that we observe it's when somebody is in need you provide (assistance) and you sort it out later," Adm. Gary Roughead, the chief of U.S. naval operations, told reporters Thursday.
Adm. Timothy Keating, commander of U.S. Pacific Command, was more blunt.
"This is perplexing. It's not helpful," he said of the port call incidents. "It's not, in our view, conduct that is indicative of a country that understands its obligations as a responsible nation."
Japan, which forms a natural arc blocking China from the Pacific, is in a highly sensitive position.
While it hosts the largest U.S. naval base overseas, Tokyo has emphasized expanded engagement with China in hopes of opening up Beijing and keeping potential flare-ups under control.
Economic cooperation has grown rapidly, but political ties continue to be colored by regional rivalry and a lingering legacy of animosity from Japan's invasion and occupation of parts of China in the 1930s and '40s.
The potential for clashes at sea is particularly high.
Japan and China have territorial disputes over gas fields in the East China Sea, and Japan depends heavily on sea lanes near China for the free passage of its oil imports from the Middle East.
Aboard the Shenzhen, Rear Adm. Xiao Xinnian said worries about China's military growth are unfounded.
"There shouldn't be any concern," he told a small group of reporters. "In my personal opinion, China's effort to modernize its military is very transparent."
He added that China's military strategy is defensive and its growth is in step with the growth of China's economy and international role.