The Chinese carrier Shandong led a group of naval vessels through the southwestern part of the strait, the ministry said in a statement.
The Taiwanese military tracked developments "with joint intelligence surveillance and reconnaissance methods" and dispatched "appropriate troops" to monitor the situation, the ministry said.
Earlier Wednesday morning, the Defense Ministry announced that it had also detected 19 Chinese aircraft near Taiwanese airspace, with two Y-8 monitoring planes entering Taiwan's air identification zone.
Beijing's incursions are the latest in a steady stream of provocations that Taipei calls "gray zone" warfare meant to strain the island's defense capabilities and wear down its morale.
China considers the democratic island of 23 million a wayward province and has vowed to seize control of it by force if necessary. Taiwan has never been a part of the mainland People's Republic of China, which was founded in 1949, and rejects Beijing's sovereignty claims.
The island has also been a growing source of friction in China-U.S. relations.
Earlier this month, a Chinese warship nearly collided with an American destroyer conducting freedom of navigation operations in the Taiwan Strait, in a maneuver that the U.S. military called "unsafe."
That incident came just days after the Pentagon said a Chinese J-16 fighter jet performed "an unnecessarily aggressive maneuver" against a U.S. aircraft operating in the South China Sea.
On Monday, U.S. Secretary of State Antony Blinken met with Chinese President Xi Jinping in Beijing and told reporters he raised concerns about China's "provocative actions in the Taiwan Strait and South and East China seas."
The United States does not recognize the island diplomatically but sells Taipei weapons. President Joe Biden has ruffled feathers in Beijing on several occasions by saying that the U.S. military would defend Taiwan against invasion attempts from China, statements that White House officials have later walked back.
Blinken reiterated Monday that Washington does not support Taiwan's independence and is "opposed to any unilateral changes to the status quo by either side."
"We remain committed to meeting our responsibilities under the Taiwan Relations Act, including making sure that Taiwan has the ability to defend itself," he added.
China previously deployed the Shandong, which was commissioned in 2019, near Taiwan in April in response to Taiwanese President Tsai Ing-wen's visit to the United States.
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