Equivalent single layer (ESL) elements provide an easy and computationally effective way to model stiffened plates in finite element analysis of ship structures. Secondary stiffeners are incorporated into the plate or shell formulation. In the free vibration analysis, these elements ignore inertia induced local deformation of plating between the secondary stiffeners. Oscillating motion causes inertia induced body load that locally deforms the plate. This local deformation may have a significant effect on the global modal frequencies of a deck structure. This paper presents a method for correcting ESL modal frequencies by modifying generalised mass and stiffness of the modes. The modification is based on the kinetic and strain energies of the local deformations. Energy components are derived from local consideration of plate in cylindrical bending under enforced support vibration. The method is validated in a case study of ship deck structure against shell mesh results, and good agreement is found.