形成2013年台日漁業協議適用海域之主要原則為日本沖繩漁連與水產廳之適用海域規劃。沖繩漁連與水產廳從日本野田政府至安倍政府時期共同形成適用海域規劃。日本政府依規劃對台灣政府談判，包括使水產廳對台灣政府談判適用海域邊界設定；並在水產廳與台灣政府發生談判僵持時，提供部份符合沖繩漁連與水產廳規劃之政策折衷。

The major principle which shaped the Designated Zone of the 2013 Taiwan-Japan Fisheries Agreement was the Designated Zone design made by Japan's Okinawa Prefectural Federation of Fisheries Cooperative Associations (JF-Okinawa) and Japan Fisheries Agency (JFA). Since the period of Japan's Noda Cabinet to that of Abe Cabinet, JF-Okinawa and JFA had been jointly designing a Designated Zone. The Japan Government then followed JF-Okinawa and JFA's design to negotiate the Designated Zone with Taiwan Government. The Japan Government had JFA to negotiate the border setting of the Designated Zone with Taiwan Government. At the point that JFA and Taiwan Government were in a stalemate, the Japan Government provided policy compromise that partly conformed to JF-Okinawa and JFA's design.