We study the robustness of the determination of the neutrino masses and mixing from the analysis of atmospheric and K2K data under the presence of different forms of phenomenologically allowed new physics in the nu_mu--nu_tau sector. We focus on vector and tensor-like new physics interactions which allow us to treat, in a model independent way, effects due to the violation of the equivalence principle, violations of the Lorentz invariance both CPT conserving and CPT violating, non-universal couplings to a torsion field and non-standard neutrino interactions with matter. We perform a global analysis of the full atmospheric data from SKI together with long baseline K2K data in the presence of nu_mu -> nu_tau transitions driven by neutrino masses and mixing together with sub-dominant effects due to these forms of new physics. We show that within the present degree of experimental precision, the extracted values of masses and mixing are robust under those effects and we derive the upper bounds on the possible strength of these new interactions in the nu_mu--nu_tau sector.