It was suggested that a tension between the mass-squared differences obtained from the solar neutrino and KamLAND experiments can be solved by introducing the non-standard flavor-dependent interaction in neutrino propagation. In this paper we discuss the possibility to test such a hypothesis by atmospheric neutrino observations at the future Hyper-Kamiokande experiment. Assuming that the mass hierarchy is known, we find that the best-fit value from the solar neutrino and KamLAND data can be tested at more than 8 $sigma$, while the one from the global analysis can be examined at 5.0 $sigma$ (1.4 $sigma$) for the normal (inverted) mass hierarchy.