The United States and its allies regularly transit the 180-kilometre (112-mile) Taiwan Strait to reinforce its status as an international waterway, angering Beijing.
Beijing has never ruled Taiwan, but it claims the democratic island as part of its territory and has threatened to bring it under its control by force.
Taipei said the US ships travelled from north to south "starting from February 10".
China's People's Liberation Army said Wednesday it had monitored the passage of the US destroyer and the ocean survey ship.
"This US action sent the wrong signal and increased security risks," Li Xi, a senior colonel and spokesman for China's Eastern Theatre Command, said in a statement.
Taiwan's defence ministry spokesman Sun Li-fang dismissed the criticism and said Taipei supported the freedom of navigation in the Taiwan Strait.
"Regarding the situation around the Taiwan Strait, there is no need for me to elaborate further on who is the so-called troublemaker," he told reporters Wednesday.
"All neighbouring countries should have a very deep understanding of this".
Washington's latest passage through the Taiwan Strait was the first time since US President Donald Trump took office in January.
It came after Trump and Japanese Prime Minister Shigeru Ishiba said on Friday they "opposed any attempts to unilaterally change the status quo (in the Taiwan Strait) by force or coercion".
Data published by the Taiwan defence ministry showed 62 Chinese military aircraft were detected near the island in the 48 hours to 6:00 am local time on Wednesday, coinciding with the US ships' transit.
"We have monitored the situation and responded accordingly," the ministry said in a statement.
Taiwan is a potential flashpoint for a war between China and the United States, which is the island's most important backer and biggest arms supplier.
In recent years, Beijing has ramped up political and military pressure on Taipei to accept its sovereignty claims, and staged multiple rounds of large-scale war games since President Lai Ching-te took office in May.
A record 153 aircraft were reported on October 15 after China staged large-scale military drills in response to Lai's National Day speech days earlier.
A week after China's drills, a US and a Canadian warship sailed through the Taiwan Strait separating the island and China.
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