We present a geometric approach for fault detection and isolation (FDI) in robotic manipulators in presence of model uncertainty. A systematic procedure is introduced for representing robotic system model being affine with respect to faults and disturbances. The proposed residual generator has smooth dynamics with freely selectable functions and it does not require high gains or threshold adjustment for the FDI purpose. No assumption on amplitude of faults and their rate is used. The solvability conditions for the FDI problem lead to a quotient observable subspace unaffected by all unknown inputs except the faults. Simulation example demonstrates localization of faults in presence of uncertainty in link moment-of-inertia matrices and measurement noise.