The fishermen lobbed eggs and clashed briefly with police while delivering a petition Wednesday at the Interchange Association, which handles relations between the two in the absence of diplomatic ties.
Taiwan has called the boat's seizure Monday about 278 kilometers southeast of Japan's Okinotori islands an illegal act, saying it was fishing in international waters at the time.
Japan has demanded the posting of a USD 54,442 bond for the release of the boat and its 10 crew members.