Both types of long and short gamma ray bursts involve a stage of a hyper-Eddington accretion of hot and dense plasma torus onto a newly born black hole. The prompt gamma ray emission originates in jets at some distance from this ‘central engine’ and in most events is rapidly variable, having a form of sipkes and subpulses. This indicates at the variable nature of the engine itself, for which a plausible mechanism is an internal instability in the accreting flow. We solve numerically the structure and evolution of the neutrino-cooled torus. We take into account the detailed treatment of the microphysics in the nuclear equation of state that includes the neutrino trapping effect. The models are calculated for both Schwarzschild and Kerr black holes. We find that for sufficiently large accretion rates (>~10M⊙ s−1 for non-rotating black hole, and >~1M⊙ s−1 for rotating black hole, depending on its spin), the inner regions of the disk become opaque, while the helium nuclei are being photodissociated. The sudden change of pressure in this region leads to the development of a viscous and thermal instability, and the neutrino pressure acts similarly to the radiation pressure in sub-Eddington disks. In the case of rapidly rotating black holes, the instability is enhanced and appears for much lower accretion rates. We also find the important and possibly further destabilizing role of the energy transfer from the rotating black hole to the torus via the magnetic coupling.