WASHINGTON (CNN) -- The United States has filed a formal protest with China over the decision to deny port visits to a U.S. aircraft carrier and two other ships last week, an incident a Pentagon spokesman Wednesday called "baffling."
The aircraft carrier USS Kitty Hawk returns to the Yokosuka U.S. naval base Tuesday.
China's military attache, Maj. Gen. Zhao Ning, received a message of "deep regret and concern" from David Sedney, the deputy assistant secretary of defense for east Asia, Defense Department spokesman Geoff Morrell said. Zhao "said nothing substantive in response but promised to relay the message back to Beijing," Morrell told reporters.
U.S. President George W. Bush also discussed the issue in a Wednesday meeting with Chinese Foreign Minister Yang Jiechi, who described the incident as "a misunderstanding," White House spokeswoman Dana Perino said.
Chinese authorities canceled a scheduled Thanksgiving port call in Hong Kong for the Japan-based aircraft carrier USS Kitty Hawk just hours before it was supposed to dock. The cancellation was "a costly inconvenience to the families who had traveled there to spend Thanksgiving with their loved ones on board," Morrell said.
And two days beforehand, Chinese authorities also denied permission for the minesweepers USS Patriot and USS Guardian to ride out a storm in Hong Kong's harbor. The Navy's Pacific Fleet commander, Adm. Timothy Keating, called that decision "more disturbing" Tuesday.
"They suffered no damage," Keating said. "But this is a kind of an unwritten law among seamen that if someone is in need, regardless of genus, phylum or species, you let them come in. You give them safe harbor. Jimmy Buffett has songs about it, for crying out loud."
China recently has expressed concerns about U.S. arms sales to Taiwan and Bush's October presentation of a Congressional gold medal to the Dalai Lama, the exiled Tibetan spiritual leader.
But Morrell said he was unaware of any "hiccups" in U.S.-Chinese military ties.
"I think that's why this incident is so baffling to us, because there is no indication at all prior to the Kitty Hawk being refused entry to the Port of Hong Kong that there was any reason or any cause for concern," he said. E-mail to a friend 
CNN's Jamie McIntyre contributed to this report.
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