The latest operation shows the U.S. Navy is increasing the pace of strait passages.
MND issued a statement in the evening saying two USA military vessels are going through Taiwan Strait, which is global waters, as a routine operation, but gave no further details about the passage.
China said Tuesday it has expressed concern to the United States over what it considered an affront to its sovereignty after two USA warships sailed through the Taiwan Strait.
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"Cruising through the Strait is not new, but it is a strong signal that the US will be on Taiwan's side in case of a crisis between Taipei and Beijing", said Jean-Pierre Cabestan, who teaches US-China relations at Hong Kong Baptist University.
"The U.S. Navy will continue to fly, sail and operate anywhere global law allows", he added.
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The Pentagon says Washington has sold Taiwan more than 15 billion dollars in weaponry since 2010.
Taiwan's defence ministry said it closely monitored the operation and was able to "maintain the security of the seas and the airspace" as it occurred. The U.S. has also accused China of engaging in cyberattacks against the U.S. government and businesses.
Beijing recently conducted a series of military manoeuvers, including a live fire exercise in the Taiwan Strait in April, declaring its willingness to confront Taiwan's "independence forces". The U.S. acknowledges China's stance but provides Taiwan with defense equipment and opposes reunification by force.
It has also viewed US overtures toward Taiwan with alarm, including its unveiling a new de facto embassy in Taiwan and passage of the Taiwan Travel Act, which encourages USA officials to visit the island.
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