The development of fishery sector in Indonesia, especially in the north coast of Java has led to a more intensive fishery product flow. The development consists of both domestic and export demand. As consequences, product quality, environment, transportation, cold chain system, and ports should bring as the basis that must be strengthened to create sustainable fisheries. In general, Indonesia fishing port has a separate system from a general port that deals with cargoes. Although in practice (especially in the Port of Tegal), fishing boats also berthing, drop off, and trade at general ports area. The disadvantage that very clearly felt by the fishermen are the lack of development of cold chain system that impact on fishery products and lowering the selling price. This article provides strategies to improve the quality of the fisheries sector through port governance system with cooperation scenarios. The main idea is general ports and national fisheries companies has a joint cooperation to build and operate cold storage facilities in the general ports area (case study at Port of Tegal). In the planning process, the general port companies invest cold storage building and machinery, while the fishing companies operate cold storage facilities. In order to know the quantitative effects of scenarios, the financial approach with NPV, and IRR components is conducted in this article. The result shows that this scenario gives IRR approximately 20%-50% for overall network. The proposed scenario is expected to provide information to various groups (such as government, decision maker, general ports companies, fishing companies, and fishermen) that integrated between general port and fish operator may give a better impact the future fishing sector especially in national fishing logistics.