Energy flow analysis has been developed and studied by many researchers to analyze acoustic energy in the medium to high frequency ranges. In this paper, a method to solve the 3D acoustic multi-domain problem by adopting an indirect approach to the EFBEM (Energy Flow Boundary Element Method) is proposed. A joint matrix comprised of power transmission and reflection coefficients is used to describe the energy exchanges between domains and absorption coefficients are applied to consider an energy absorbing boundary condition. Finally, coupled small reverberation rooms and a mock-up system of ship cabins were analyzed using the method to compare the numerical analysis with the experimental results. They show good agreement, thereby validating the method. The indirect EFBEM method allows us to use spherical wave Green's functions, which are not available in the direct method. Therefore, it is expected that the method can be applied to almost any acoustic multi-domain situation, from room to room cases to radiation problems.