This paper presents a methodology that allows to automate the model-based generation of system FMEA for which some components' behaviors are not precisely known. Using simple assumptions on the relations that may exist between the input and output of such components, the deviation of the system from its nominal behavior brought by failure modes is inferred and used to identify the possible failure of its functions. The presented work is applied to an electromechanical system involving a controller whose exact behavior is assumed to be unknown.