We report on experiments performed at low temperatures on aluminum covered silicon nanoelectromechanical resonators. The substantial difference observed between the mechanical dissipation in the normal and superconducting states measured within the same device unambiguously demonstrates the importance of normal-state electrons in the damping mechanism. The dissipative component becomes vanishingly small at very low temperatures in the superconducting state, leading to exceptional values for the quality factor of such small silicon structures. A critical discussion is given within the framework of the standard tunneling model.