Illegal Unregulated Unreported (IUU) fishing threatens marine biodiversity and associated economic values. Recognizing this, the Indonesian government exercises a tough anti IUU fishing policy. The policy generates both success stories and failure issues. Biological parameters are better: disappeared species returned, catch per unit effort CPUE increased, fish size becomes larger, fishing trips are shorter. However, data show that the stock utilization is not optimum, fishing discard is high, and fishers’ income remains low. This study is aimed to formulate measures necessary to minimize side effects. Data were collected from selected landing places. It is concluded that the most notable factors causing detrimental side effects are lack of carrier vessels, inadequate cold handling infrastructure, poor processing facilities, and high shipping costs. Among complementary policy options, the most strategic one is integrating the anti IUU fishing policy with the national marine toll program. This paper also suggests that more frequent shipping and larger quota should be allocated by the program for transporting marine products from the production centers to processing, export, and consumer locations.