One way to assess the uncertainty in fatigue damage analysis is to use a so-called safety index. In the computation of such an index the variation coefficient for the accumulated damage is required. In this paper the expected fatigue damage and its coefficient of variation is firstly estimated from measured stress. Secondly, when suitable stress measurements are not available these are computed from models for damage accumulation and sea states variability. Stresses during ship sailing period are known as the non-stationary, slowly changing, Gaussian processes and hence damage accumulation, during encountered sea state, can be approximated by an algebraic function of significant wave height, ship speed and heading angle; Further the space time variability of significant wave height is modeled as a lognormal field with parameters estimated from the satellite measurements. The proposed methods to estimate uncertainties in the damage accumulation process are validated using full scale measurements carried out for a container vessel operating in the North Atlantic.