Self-diffusion in non-stoichiometric intermetallic compounds with the B2 and structures has been considered. It was shown that the thermal and compositional anti-structure defects substantially affect the diffusivity forming `anti-structural bridges' for a vacancy migration without additional disordering of the intermetallic compound. While this contribution was found to have a percolation nature for both sublattices in the case of the B2 structures, the percolation is to be taken into account only for diffusion of the minor element in intermetallic compounds with the structure. The numerical calculations were carried out for the CoGa triple-defect intermetallic compound. Critical exponents and fractal characteristics of percolation clusters were estimated. Values of the threshold anti-structure defect concentrations are for B2 structures and for the -sublattice of the compound with the structure. Owing to the temperature dependence of defect concentration the percolation threshold is temperature dependent also and, e.g., corresponds to composition at T = 1323 K. The theoretical predictions are compared with experimental data.