As an archipelagic country, Indonesia needs ferry transportation to connect and support the economic activities between areas bounded by the sea. The famous crossing route is the Merak–Bakauheni one, which connects the Java and Sumatra economic corridors. Many ships operate on this route, but limited port facilities significantly affect the efficiencies of the services provided, hence, they have to be moved. Therefore, this research analyzed the suitability of ships to operate on the eastern crossing. The analysis method used the financial aspect (revenue) feasibility, the suitability of the port infrastructure, and the oceanographic conditions. The financial analysis used the ships’ operating cost method to determine the crossing passage rates based on their specifications. It simulated the ships with various load factors to identify potential gains or losses. Furthermore, the infrastructure suitability analysis used the under keel clearance and comparative methods to compare the suitability of the ship dimensions and tonnage with the port infrastructure capacity. The oceanographic analysis used the Weibull method to simulate the redefinition of the distribution of significant wave heights, which was compared with the ratio of the ship dimensions and wave slope to determine its heel angle using the IMO Weather Criterion method (IS Code 2008). The results showed that the relocation of ships from the Merak–Bakauheni route directly to Eastern Indonesia through the existing crossing routes is feasible from the aspect of shipping safety, but it is not feasible financially or in terms of infrastructure. The Benoa–Labuan Bajo route is a potential new route recommendation, with regulatory support for the operation of ships in the form of tariffs and operational costs, and it permits the use of subsidized fuel. On the other hand, ship owners must consider modifying the ramp door to suit the port wharf structure.