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A new formulation for the modular construction of flexible multibody systems is presented. By rearranging the equations for a flexible floating body and introducing the appropriate canonical momenta, the model is recast into a coupled system of ordinary and partial differential equations in port-Hamiltonian (pH) form. This approach relies on a floating frame description and remains valid under the assumption of small deformations. This allows including mechanical models that cannot be easily formulated in terms of differential forms. Once a pH model is established, a finite element based method is then introduced to discretize the dynamics in a structure-preserving manner. Thanks to the features of the pH framework, complex multibody systems are constructed in a modular way. Constraints are imposed at the velocity level, leading to an index 2 quasi-linear differential-algebraic system. Numerical tests are carried out to assess the validity of the proposed approach.