The service life of a ship depends on its structural integrity, which can be undermined through time via different loading conditions. The incorporation of a Structural Health Monitoring (SHM) system could enhance the safety of the vessel because information about its health condition could potentially lead to the avoidance of catastrophic scenarios by the detection of structural damages and their progression, especially when they may be unobservable via physical inspection. Within this context, a model-based SHM method called inverse Finite Element Method (iFEM) has been recently developed to assess the displacement and stress profile of vessels. iFEM offers several advantages, including the independence from material properties and loading conditions, the lack of training procedures, and the limited computational demand, which makes it suitable for real-time applications, enabling to reconstruct the complete displacement, and thus, the strain field starting from discrete strain measures. In this work, we explore the application of the iFEM in challenging scenarios, regarding repeated stress fluctuations (e.g. fatigue) or other type of mechanisms like corrosion, buckling or even externally imposed damages from collision impacts or combat type damages (explosions, ballistic, etc.), depending on the specific case of naval vessels. An anomaly index is used to highlight the health state of the structure by comparing the strain predicted by the iFEM at some test locations with the strain measured by a test sensor in the same position. The two values will match only for the healthy structure, while their departure from each other will indicate anomalous conditions. Though the formulation of the diagnostic problem is general for an arbitrary component geometry and damage type, the proposed study is accompanied by some numerical examples applied to a realistic ship case.