The accidental launch of the domestically developed Hsiung Feng III anti-ship missile from a naval base in Kaohsiung, south of the island, took place as Taiwan's President Tsai Ing-wen, also commander-in-chief of the armed forces, was overseas.
The missile, with a range of 300 kilometres, flew about 75 kilometres before plunging into waters off Penghu, a Taiwanese -administered island in the Taiwan Strait.
"The missile was launched by operational error. We are investigating the case," Vice-Admiral Mei Chia-hsu of the Taiwanese Navy was quoted as saying by the Hong Kong-based South China Morning Post.
Asked if the incident risked a misunderstanding with Beijing, Mei said the navy had reported the incident to the island's defence ministry, which would handle the case accordingly.
Meanwhile in Beijing, Taiwan figured prominently in a speech by President Xi Jinping to a rally to mark the 95th anniversary of the Communist Party of China (CPC), where he said China is firmly opposed to Taiwan's independence.
"We firmly oppose the 'Taiwan independence' secessionist activities," Xi said at the ceremony.
"More than 1.3 billion Chinese people and the whole Chinese nation will by no means tolerate secessionist activities by any person, at any time and in any form," he said.
China claims Taiwan as part of the mainland despite the 1949 estrangement.
Relations between the two sides which showed significant improvement in recent years took a hit after election of Tsai, who defeatedMa Ying-Jeou who promoted normalisation of ties between the two sides in recent election.
The Taiwanese missile did not pass the mid-course line of the Taiwan Strait, Mei said, which meant it was not aimed at Fujian province, which lies on the other side of the strait.
Mei said the Chinchiang (PCG-610) patrol ship was undergoing a drill inspection when officers failed to follow standard operating procedures and launched the missile by mistake.
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