The incident comes after US President Joe Biden ordered the shooting down of a Chinese balloon after it crossed US territory, including over areas with sensitive military sites.
US officials said it was a surveillance balloon and part of a fleet of such craft allegedly floating around the globe.
Beijing insists it was a meteorological craft that had blown off course and has accused Washington of sending similar devices into its airspace, charges the US has denied.
Taiwan's army said "unidentified objects" were spotted falling from the sky on Thursday over the Matsu islands, some 280 kilometres from capital Taipei.
There they found the remains of a balloon that was one meter in diameter and a device inscribed with simplified Chinese characters commonly used in China that read "Taiyuan Radio No. 1 Factory Co., Ltd." and "meteorology instrument," the army said in a statement.
"Our initial analysis is that the remains belong to a meteorological detection device which have been stored by relevant units to be further analysed," the army said.
"All units are required to enhance camp patrols and continue to... monitor relevant situation."
Beijing has ramped up military, diplomatic and economic pressure in recent years on Taiwan, which China claims as part of its territory and has vowed to seize one day, by force if necessary.
Taiwan's defence ministry said at a press conference on Tuesday that Chinese meteorological balloons had previously been spotted without providing details on the number and frequency.
The ministry said it would shoot down devices that pose a "high level of threat" but it has not yet encountered such a craft.
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