Yeh Mei, a 33-year-old lieutenant with the Military Intelligence Agency, had been put on Taiwan's wanted list after failing to return for duty following an overseas trip in 2012.
Yeh confessed to seeking permission from her superior for a sightseeing trip to Thailand with the intention of deserting her duties because she could not adjust to a military career, and fled to Britain via Bangkok in June 2012, prosecutors said in a statement.
The offence is punishable by a maximum five-year jail term.
She had claimed that she could be sentenced to death and sought political asylum with the British authorities, but the bid was rejected and she was deported last month for overstaying her visa.
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When Yeh first disappeared, there was speculation in Taiwan's media that she may have joined China's spy network. Taiwan's Military Intelligence Agency has attributed Yeh's disappearance to "personal factors".
Taiwan and China have spied on each other ever since they split in 1949 at the end of a civil war. Beijing still regards the self-ruled island as part of its territory awaiting reunification.