The US Navy, occasionally accompanied by ships from allied countries, transits the strait about once a month. China, which claims Taiwan as its own territory, says the strategic waterway belongs to it.
The US Navy said the vessels were the Arleigh Burke-class guided-missile destroyer USS Ralph Johnson and Pathfinder-class survey ship, USNS Bowditch. The ships carried out a north-to-south transit February 10-12, it said.
"The transit occurred through a corridor in the Taiwan Strait that is beyond any coastal state's territorial seas," said Navy Commander Matthew Comer, a spokesperson at the US military's Indo-Pacific Command.
"Within this corridor all nations enjoy high-seas freedom of navigation, overflight, and other internationally lawful uses of the sea related to these freedoms."
China's military said that Chinese forces had been dispatched to keep watch.
"The US action sends the wrong signals and increases security risks," the Eastern Theatre Command of the People's Liberation Army said in a statement.
China considers Taiwan its most important diplomatic issue and it is regularly a stumbling block in Sino-US relations.
China this week complained to Japan over "negative" references to China in a statement issued after a meeting between Trump and Japanese Prime Minister Shigeru Ishiba.
That statement called for "maintaining peace and stability across the Taiwan Strait", and voiced support for "Taiwan's meaningful participation in international organisations".
Asked in Beijing on Wednesday about the US warships, Zhu Fenglian, spokesperson for China's Taiwan Affairs Office, said that Taiwan was a "core interest" for the country and that the United States should act with caution.
"We are resolutely opposed to this and will never allow any outside interference, and have the firm will, full confidence and capability to uphold the country's sovereignty and territorial integrity," she said.
Taiwan's defence ministry said its forces had also kept watch but noted the "situation was as normal".
China's military operates daily in the strait as part of what Taiwan's government views as part of Beijing's pressure campaign.
On Wednesday, Taiwan's defence ministry said it had detected 30 Chinese military aircraft and seven navy ships operating around the island in the previous 24-hour period.
"I really don't need to explain further who is the so-called troublemaker around the Taiwan Strait. All other countries in the neighbourhood have a deep appreciation of this," ministry spokesperson Sun Li-fang told reporters in Taipei.
Chinese state television said on Wednesday that since Lunar New Year's Eve on January 28, the Eastern Theatre Command had repeatedly dispatched sea and air forces to carry out "combat readiness" patrols and training missions around Taiwan.
The operations aim to "guard the joy and peace of the people on both sides of the Taiwan Strait", the report said.
The last time a US Navy ship was confirmed to have sailed through the strait was in October, a joint mission with a Canadian warship.
Taiwan President Lai Ching-te rejects Beijing's sovereignty claims, saying only Taiwan's people can decide their future.
