In this paper a model updating algorithm is presented to estimate structural parameters at the element level utilizing frequency domain representation of the strain data. Sensitivity equations for mass and stiffness parameters estimation are derived using decomposed form of the strain-based transfer functions. The rate of changes of eigenvectors and a subset of measured natural frequencies are used to assemble the sensitivity equation of the strain-based transfer function. Solution of the derived sensitivity equations through the least square method resulted in a robust parameters estimation method. Numerical examples using simulated noise polluted data of 2D truss and frame models confirm that the proposed method is able to successfully update structural models even in the presence of mass modeling errors.