System identification offers ways to obtain proper models describing a ship’s dynamics in real operational conditions but poses significant challenges, such as the multicollinearity and generality of the identified model. This paper proposes a new physics-informed ship manoeuvring model, where a deterministic semi-empirical rudder model has been added, to guide the identification towards a physically correct hydrodynamic model. This is an essential building block to distinguish the hydrodynamic modelling uncertainties from wind, waves, and currents – in real sea conditions – which is particularly important for ships with wind-assisted propulsion. In the physics-informed manoeuvring modelling framework, a systematical procedure is developed to establish various force/motion components within the manoeuvring system by inverse dynamics regression. The novel test case wind-powered pure car carrier (wPCC) assesses the physical correctness. First, a reference model, assumed to resemble the physically correct kinetics, is established via parameter identification on virtual captive tests. Then, the model tests are used to build both the physics-informed model and a physics-uninformed mathematical model for comparison. All models predicted the zigzag tests with satisfactory agreement. Thus, they can indeed be considered as being mathematically correct. However, introducing a semi-empirical rudder model seems to have guided the identification towards a more physically correct calm water hydrodynamic model, having lower multicollinearity and better generalization.