A method for a reliable estimate of uncertainties and associated covariances of integral cross sections obtained via model calculations is proposed. The method accounts for uncertainties of model parameters, the numerical implementation errors and the model deficiencies, where emphasis is given on the latter one. Covariance matrices for phenomenological models as well as for almost parameter‐free microscopic calculations are obtained on the same footing. In a schematic example the method is applied for the determination of the contribution of model deficiencies associated with the optical model and multistep reaction models to the covariance matrices of 56Fe.