The USS Antietam and USS Curtis Wilbur sailed north through the Taiwan Strait Monday.
Taiwan's premier William Lai said during a parliamentary session Tuesday that Taiwan respected the United States right of passage in worldwide waters and recognised "the various efforts of the USA in maintaining peace in the Asia-Pacific Region".
China's foreign ministry has since responded, "expressing concern" at the presence of US warships in the strait.
"The Ministry of National Defense said today that two U.S. ships have sailed from the south to the north through the Taiwan Strait", said a translation of the statement.
Taiwan late on Monday requested that China refrain from interfering in its elections, saying that Beijing should respect and learn from its democracy.More news: CCTV Clip Shows Khashoggi's Alleged 'Body Double' in Identical Clothes
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In July, the Navy sent two 7th Fleet destroyers into the straits for what Pacific Fleet officials described as a "routine transit", the first time it had done so since July 2017.
"The U.S. Navy will continue to fly, sail and operate anywhere global law allows", he added. Beijing regards Taiwan as a breakaway province to be taken back, by force if necessary.
Taiwan's Defense Ministry first confirmed the transit in a statement.
Military experts say the balance of power between Taiwan and China has shifted decisively in China's favour in recent years, and China could easily overwhelm the island unless USA forces came quickly to Taiwan's aid.
While the US and China cooperate in denuclearizing North Korea, tensions have increased as both the USA and China have engaged in a trade war. The U.S. continues to sell military weapons to the island nation even though it does not have diplomatic relations with Taiwan.
China has also alarmed Taiwan by ramping up military exercises this year, including flying bombers and other military aircraft around the island and sending its aircraft carrier through the narrow Taiwan Strait separating it from Taiwan.