1949 年5 月20 日台灣展開長達三十八年的戒嚴體制。在此體制下，軍警尤其是台灣省保安司令部，從港口、機場全面介入海關查緝走私的權力。軍方以「基隆高雄兩港船舶進出口手續及檢查辦法」為權力基礎，在通商口岸成立以聯合檢查處，直接干涉海關的緝私作業，並以港口司令部監控船舶的進出，甚至要求檢查海關及港務局的作業船隻等。這些措施不僅直接衝擊海關的緝私權，並對於極需高度機動性的海關巡緝艦艇，產生莫大的滯礙，進而影響海關的海上緝私成效。在此時代背景下，台灣的緝私組織明顯呈現多頭現象，海關的海上緝私武力相對不受重視。如政府遷台後的二十六年間，海關巡緝艦艇幾乎全部沿用戰前的設備，以及海軍淘汰的軍艦三艘，這些艦艇不僅老舊缺乏機動力，而且維修成本高，多半處於停駛的狀態。事實上，長達二十餘年間，海關僅擁有1-2 艘的巡緝艦負起全台的沿海巡緝，因此當走私型態從港內零星偷渡轉變為貨櫃掉包、夾藏，以及外海漁船闖關、接駁時，海關緝私能力就備受挑戰。而緝私成效明顯不彰，也埋下日後海關巡緝艦艇被移撥給海巡署的因子。

Martial law was declared in Taiwan on May 20(superscript th), 1949, and had lasted thirty eight years since then. During this period, the military and the police, especially Taiwan Provincial Security Command, were given full power to crack down on smuggling activities in replacement of the customs in seaports and airports. The military took "Regulations Governing Import/Export Procedures and Inspection in Keelung and Kaohsiung Harbors" as the basis of its power, and set up unified inspection offices in trade ports which directly intervened in the customs authorities' anti-smuggling enforcement. These practices not only harmed the customs' authorities, but also hampered the customs' anti-smuggling patrol boats which often required high mobility. Given the above background, Taiwan's anti-smuggling authorities had been branched out, and the customs' maritime force was relatively neglected. For example, during the twenty six years after the nationalist government came to Taiwan, the custom was still using pre-war boats and decommissioned navy ships. These vessles were very aged and difficult to maintain, and most were not even seaworthy. In fact, for more than twenty years, the customs had only one or two boats used to patrol Taiwan's entire coastline. Therefore, when smuggling activities increased and grew in scale and scope, the customs' anti-smuggling ability was often put to test. The low efficiency in smuggling crackdown eventually resulted in the customs' boats being taken over by the Coast Guard Administration.