Because the NCPFS's authority is limited to promoting events, and more than ten different agencies are involved in managing the waters around Taiwan, many cross-departmental problems can only be resolved through mediation by the Executive Yuan's Ocean Affairs Committee.
由於體委會在權責上只負責活動推動，而台灣海洋管理的單位多達十多個，許多跨部會問題只有靠行政院的「海洋事務推動委員會」協調，體委會也使不上力。