The article presents a continuation of research carried out concerning identification of energy consequences of mechanical fatigue within a propeller shaft in a rotating mechanical system, while working under conditions of the loss of the required alignment of shaft lines. Experimental research was carried out on a physical model reflecting a full-sized real object: i.e., the propulsion system of the ship. It is proven, by means of an active experiment, that changes in propeller shaft deflection are reflected in the amount of dissipated kinetic energy of masses in rotational motion and the accumulated internal energy in its construction material. Adoption of a high-cycle fatigue syndrome, consisting of diagnostic symptoms determined from the action of the propeller shaft associated with the transformation of mechanical energy into work and heat, as well as with the generation of mechanical vibrations and elastic waves of acoustic emission, is proposed. To assess the diagnostic information quantity brought about by the defined features of propeller shaft fatigue, an experimental research program was developed and implemented, in which two statistical hypotheses are verified: the significance of the impact of the values enforcing the fatigue process, presented in the first part of the article, and the adequacy of the regression equation describing the fatigue durability of the propeller shaft in the energy aspect, constituting the second part of the article. This finally gives us the opportunity, after the appropriate translation of the model test results into full-sized real objects, to develop a methodology to diagnose marine propeller shaft fatigue in operating conditions. The third part of the article is devoted to this issue