The European Commission and International Maritime Organisation are looking into measures for reducing greenhouse gases and pollutants emissions of existing ships. Retrofitting of candidate vessels of the current fleet with green ship technologies is being considered. Aside ethical and political considerations, there is a need to present and explain choices of ships, technologies and policy directives with rational economic analysis. This papers studies and proposes the cost centres on which such an analysis should be based. Cost variables and parameters form the basis for building an economic assessment module that analyses private and social cost benefits of various technology measures. This study aims at developing such a module as part of the European FP-7 project Retrofit. The methodology seeks to narrow down cost variables to sensitive cost centres. It emphasises the importance of distinguishing between investment and running cost of new technology to ease policy implementation and fairness. Changes in voyage costs stems from a detailed analysis of a particular ship’s operational profile. Since ships are not classified by a distribution of their running costs, a generalized application from the benchmark using statistical parameters cannot yet be made. We extrapolate using cost parameters from shipyards and operators based on the energy consumption of vessels.