The main objective of this paper is to perform a comparative analysis between fuel consumption and CO2 emissions estimation and actual fuel consumption. A few years ago, detailed actual fuel consumption reports were collected from ship owners for determining the expenses on each trip but these reports were not publicly available. Nowadays ship owners report specific data including fuel consumption and CO2 emissions as per the requirements of EU MRV regulation. As a consequence, EMSA/MRV‐THETIS database is publicly available and provides annual reports of fuel consumption and CO2 emissions. The current study follows the bottom‐up methodology presented in detail in a recent publication where the fuel–energy consumption and air emissions (CO2, SOX, NOX, PM) of ships were calculated and presented for previous years. A detailed comparative analysis of results from calculated methodology and reported emissions data from EMSA/MRV‐THETIS database (MRV) was performed, which showed that there was a small difference in the results (about 6–12%), proving the reliability of the bottom‐up methodology for this geographic area and ships in study. © 2022 Society of Chemical Industry and John Wiley & Sons, Ltd.