The vessel, "Tung Sheng Chi 16", from Pingdong in southern Taiwan, had turned back as one of its mainland fisherman had had an asthma attack, when it was chased and seized early Monday by a Japanese vessel in waters near Okinotori Atoll, some 1,700 kilometers south of Tokyo.
Japanese personnel boarded the boat and took the captain to the Japanese ship where he was held.
The captain has not returned to the fishing boat yet and the condition of the fishermen, including the sick man, was unclear, said a source with the local fishermen's association in Pingdong on Tuesday afternoon.
Representatives of fishermen's associations across the island are expected to protest outside the office of the Japanese interchange association in Taipei on Wednesday.