We present a method to numerically compute accurate tunnelling rates for a Bose-Einstein condensate which is described by the nonlinear Gross-Pitaevskii equation. Our method is based on a sophisticated real-time integration of the complex-scaled Gross-Pitaevskii equation, and it is capable of finding the stationary eigenvalues for the Wannier-Stark problem. We show that even weak nonlinearities have significant effects in the vicinity of very sensitive resonant tunnelling peaks, which occur in the rates as a function of the Stark field amplitude. The mean-field interaction induces a broadening and a shift of the peaks, and the latter is explained by an analytic perturbation theory.