The nucleon-pion-state contribution to QCD two- and three-point functions used in the calculation of the axial form factors of the nucleon are studied in chiral perturbation theory. For physically small quark masses the nucleon-pion states are expected to dominante the excited-state contamination at large euclidean time separations. To leading order in chiral perturbation theory the results depend on two experimentally well-known low-energy constants only and the nucleon-pion-state contribution can be reliably estimated. The nucleon-pion-state contribution to the axial form factor $G_{\rm A}(Q^2)$ is at the 5 percent level for source-sink separations of 2 fm and shows almost no dependence on the momentum transfer $Q^2$. In contrast, for the induced pseudo scalar form factor $G_{\rm P}(Q^2)$ the nucleon-pion-state contribution shows a rather strong dependence on $Q^2$ and leads to a 10 to 40 percent underestimation of $G_{\rm P}(Q^2)$ at small momentum transfers. Applying the ChPT results to recent lattice data generated by the PACS collaboration we find agreement with experimental data and the predictions of the pion-pole dominance model.