A formulation is presented for the assessment of the CO2 generated by ships in operation and their evolution with time, conditional on the current legislation using Markov chains. Any potential deep repair or retrofitting of the ship propulsion system or enhancement of route operational characteristics during the service life are not accounted for. The Markov transition matrix is defined based on the ship operations and CO2 history of A, B, C, D, and E carbon intensity indicator (CII) rates. The transition between different CII rate states in the survey data is used to estimate the probability of transition of the analysed ships between different CII grates. Distinct transition matrices employing the progressively tightened legislation of CII are employed and analysed. In addition, the transition matrices can be fed into risk-based models that take the CII rates as input for defining the most appropriate ship energy efficiency management plan.