This paper aims to assess the direct economic impact on the maritime sector from its inclusion in the European Union-Emission Trading System (EU-ETS). The Monitoring, Reporting and Verification (MRV) data are analysed for the estimation of carbon dioxide (CO2) emissions within the European Economic Area (EEA). The economic impact assessment model used is scenario-based, and includes different price incentives, geographical coverage and emission allowances allocation methods. According to our findings, in case the emission allowances are fully auctioned or partially free allocated on the basis of a uniform benchmark, the increased costs would be disproportional among the maritime segments. Such a scheme would penalise Roll-on/Roll-off (RoRo) and Roll-On/Roll-Off/Passenger (RoPax) segments due their high fuel consumption per transport work in relation to oil tankers and bulkers. The establishment of differentiated benchmarks per segment seems to be a prerequisite for the effective inclusion of shipping in the EU-ETS that will reward energy efficient vessels in each segment and avoid competition distortion within the maritime industry.