The unbalance response analysis is one of the essential area in the forced vibration analysis of rotor bearing systems because of it usefulness in balancing and diagnosis as well as identification of parameters involved in rotor bearing systems. However some unbalance responses are not measurable due to the fact that rotor bearing systems are often encapsulated by fixtures or safety protectors. In the present paper, an efficent estimation scheme for unmeasured unbalance responses in rotor bearing systems is developed. The fundamental fearture of the proposed method is characterized by the linear formulae to estimate the unbalance responses from the measured unbalance responses and the finite element auxilliary model equation which is constructed to be identical to the prototype excluding the uncertain parameters such as bearing coefficients. The identification formulae for bearing parameters are also derived by using the unbalance response and the finite elements auxiliary model. Simulation is provided to verify the effectiveness of the proposed method.