On Thursday, a Pentagon press secretary said the US had sent a formal protest to Beijing over China's actions.
Geoff Morrell said that the Chinese decisions had been "baffling" and that "we are expressing officially our displeasure".
The issue of the port visits was also brought up at the White House on Wednesday during talks between George Bush, the US president, and Yang Jiechi, the visiting Chinese foreign minister.
Yang reportedly told Bush the case of the Kitty Hawk was based on a "misunderstanding", a White House spokeswoman said, although no mention was made of the barred minesweepers.
'Disturbed and harmed'
However, on Friday, Liu Jianchao, a Chinese foreign ministry spokesman, said the report from Washington that quoted Yang as calling the incident a "misunderstanding" was incorrect.
Liu said ties had been "disturbed and harmed" by "erroneous" US actions and that "the report is not in line with the facts".
On Thursday a Chinese communist party-owned newspaper had hinted at the possible cause of the row, blaming a US decision to sell anti-missile defence system to Taiwan.
Citing an unnamed colonel in the Chinese military, it said the decision "obviously sent the wrong signals" to Taiwan's leaders, who Beijing accuses of seeking to declare formal independence.
"At a time when the US side is seriously harming China's interests, there is no logic under heaven by which China should then be expected to open its heart and embrace him," the paper said.
Meanwhile, Japan has scrapped a plan to allow Chinese navy officers to tour a destroyer equipped with US high-tech Aegis radar equipment.
Japan's Yomiuri newspaper said the captain and senior crew members of the Chinese warship Shenzhen, which docked in Tokyo this week on a landmark visit symbolising warmer Sino-Japanese ties, were to visit the ship, but the plan was scrapped at the request of US officials.
However, a US embassy spokesman denied any US role in the decision.
David Marks said: "Neither the US Forces in Japan nor the US embassy in Tokyo asked the Government of Japan to cancel a tour of a Japan Maritime Self-Defence Force Aegis ship by PLA (People's Liberation Army) Navy officers."
Shigeru Ishiba, Japan's defence minister, said he had not heard that a tour of the destroyer had been scrapped at the request of the US, but added that the need to protect classified data was a factor in deciding what to open up.
He said: "Various options were considered by those in charge. There is the situation of trust, but at the same time there is the matter of protecting confidential information, and the question is how to balance those."