The 1999 Korea-Japan Fisheries Agreement provides for the so-called "Intermediate Waters" on the East Sea (or the Sea of Japan) in Article 9. The Zone was established as a kind of provisional arrangement as a result of the difficulties in negotiating maritime boundaries due to the territorial controversy between Korea and Japan. This kind of special waters could exert negative effects upon the legal status of Dokdo therein and its peripheral waters.
It's because the "Intermediate Waters" is above all incompatible with exclusiveness of Korean jurisdiction in peripheral zone of Dokdo, especially through common or shared exercise of fishing rights by Korea and Japan and by establishing joint management system by Korea-Japan Joint Fisheries Commission in the waters.
To be brief, "Intermediate Waters" could be said to weaken the exclusive territorial claim of Korea over Dokdo. Inasmuch as Dokdo is located in the Intermediate Zone, it appears that Dokdo has now emerged as more of a disputed territory by the 1999 Fisheries Agreement than before. To maintain or consolidate territorial claim over Dokdo, the South Korean government should denunciate the present Korea-Japan Fisheries Agreement as soon as possible and conclude a new agreement ruling out "Intermediate Waters"