This study discusses the problem of determining which container port should be developed within an existing network and when this should be carried out. A case study of Indonesia’s port network is presented, where several new ports are to be improved to ensure smooth interisland transportation flows of goods. The effects of the investment on economic consequences and increased network connectivity are assessed. When improving the ports, we consider that the available budget limits the investment. The network connectivity is evaluated by considering the number of reachable ports from the developed ports or transportation time required from other ports within the same port cluster. Based on our knowledge, our study is the first one that discusses the investment problem in multiple container ports under single management, as well as its effects regarding the increase in container flows. The problem is introduced and three mathematical models are proposed and used to solve a real problem. The results show that different models have different improved aspects of container transportation flows—e.g., a balanced improvement of the whole port network (Model 2) and appropriate investment priority for port clusters (Model 3).