The man, surnamed Ruan, was picked up by Taiwan's coast guard in June after his vessel collided with other boats on the Tamsui River, which flows from the capital Taipei to the island's northern coast.
Officials said he was one of 18 purported defectors from China -- which claims Taiwan as part of its territory -- seen over the past year or so.
They all claimed to admire Taiwan's "democratic way of life", authorities said, who also warned they could not rule out the possibility the incursions were a test of the island's defences by China.
Ruan, 60, identified by Taiwanese authorities as a former captain in the Chinese navy, reportedly told coast guard officers at the scene that he wanted to "defect".
The Shilin District Prosecutors Office on Wednesday charged him with violating a law governing relations with China and also for entering Taiwan without permission.
"The defendant smuggled himself to Taiwan by boat due to personal reasons... no involvement of military or national security crimes was found," it said in a statement.
China has in recent years ramped up military and political pressures on the island, while Beijing has severed all top-level communications since 2016.
Tensions have spiked under two consecutive Taipei administrations -- first under former leader Tsai Ing-wen, and now under President Lai Ching-te -- which have refused to acknowledge China's claim on Taiwan.
Relations have been further marred since February following a string of fishing boat incidents -- including one in July when a Taiwanese vessel carrying five people was seized by the Chinese coast guard for allegedly fishing illegally off the coast of China's Fujian province.
Taiwan's Fisheries Agency insisted that the area where the incident took place was a traditional fishing ground for both sides.
The Mainland Affairs Council, which handles cross-strait issues, confirmed Wednesday that one Taiwanese and three Indonesian crew members were repatriated the day before.
However the captain of the boat was not released, and the MAC urged China to release the captain and return the fishing boat to Taiwan "as soon as possible", it said in a statement.
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