The problem addressed here is the application of model-based fault detection algorithm to active control of flexible structures. The modeling of mechanical structures with the finite element (FE) method leads to high order models which must be reduced. This step introduces important uncertainties which make necessary the use of robust fault detection and diagnosis (RFDD) algorithms. Here, we propose to apply a RFDD method using the H2 and H∞ polynomial estimation to estimate the input fault signal. To illustrate the efficiency of this method, it is applied to a composite beam with piezoelectric patches as sensors and actuators.