Black hole (BH)-torus systems are promising candidates for the central engine of γ-ray bursts (GRBs), and also possible outcomes of the collapse of supermassive stars to supermassive black holes (SMBHs). By three-dimensional general relativistic numerical simulations, we show that an m = 1 nonaxisymmetric instability grows for a wide range of self-gravitating tori orbiting BHs. The resulting nonaxisymmetric structure persists for a time scale much longer than the dynamical one, becoming a strong emitter of large amplitude, quasiperiodic gravitational waves. Our results indicate that both, the central engine of GRBs and newly formed SMBHs, can be strong gravitational wave sources observable by forthcoming ground-based and spacecraft detectors.