Taiwan's defence ministry said in a statement late that the voyage of the US vessels was in accordance with regulations. The move will likely be viewed in Taiwan as a sign of support from US President Donald Trump's government.
China urges the United States to prudently and properly handle the Taiwan-related issues, according to Chinese Foreign Ministry spokesman Geng Shuang on Thursday.
Geng made the comments in response to the passage by two US warships through the Taiwan Strait on Wednesday.
He said China has closely monitored the passage from start to end and expressed its concerns to the US side.
"The Taiwan issue concerns the sovereignty and territorial integrity of China and is the most important and sensitive issue in China-US relations," Geng said.
"We urge the US side to strictly abide by the one-China principle and the stipulations of the three China-US joint communiques, prudently and properly handling Taiwan-related issues so as not to harm China-US relations as well as the peace and stability across the Taiwan Strait," he added.
The voyage risks further heightening tensions with China, which considers Taiwan its own and has not ruled out the use of force to bring the self-ruled island under its control.
Taiwan's defence ministry said in a statement late on Thursday the ships were moving in a northerly direction and that their voyage was in accordance with regulations.
It said Taiwan closely monitored the operation to "ensure the security of the seas and regional stability".
The move will likely be viewed in Taiwan as a sign of support from US President Donald Trump's government amid growing friction between Taipei and Beijing.
China has stepped up pressure on Taiwan since President Tsai Ing-wen, from the pro-independence ruling party, took office in 2016. It has regularly sent military aircraft and ships to circle the island on drills in the past few years.
Beijing sent several bombers and aircraft through the Bashi Channel, which separates Taiwan from the Philippines, earlier on Thursday, Taiwan's defence ministry said in a separate statement.
A similar Chinese operation was conducted on Tuesday, the ministry said, and both were monitored closely.
Chinese President Xi Jinping said in early January China reserves the right to use force to bring Taiwan under its control. In response, Tsai vowed to defend the island's democracy and called for international support to protect Taiwan's way of life.
Trump recently signed into law the Asia Reassurance Initiative Act reaffirming the US commitment to Taiwan, including arms sales.
Washington has no formal ties with Taiwan but is bound by law to help it defend itself and is its main source of arms.