In this letter we report the direct perturbative QCD evaluation of twist-4 effects in diffractive DIS. They are large and have a strong impact on the $Q^2$ dependence of diffractive structure functions at large $beta$. Based on the AGK rules, we comment on the possible contribution from diffractive higher twists to $propto {1 over Q^{2}}$ corrections to proton structure function at small $x$. These corrections to the longitudinal structure function $F_{L}$ may be particularly large.