When analyzing the seismic response of a very long elevated structure such as a Shinkansen viaduct, it is common practice to analyze a cutout of the structure under consideration and treat its both ends as free boundaries. This is attributable to the assumption that seismic response analysis assuming free boundary conditions is more conservative than one assuming non-free boundary conditions. In this study, after finding out that response to harmonic ground motion can be greater than under free-boundary conditions if outward energy dissipation occurs from the analysis domain, a series of numerical experiments was performed to determine whether such phenomena occur in seismic response. Then, after confirming that the frequency components of ground motion that satisfy the wave propagation condition greatly affect seismic response, the study showed that the area of the wave propagation condition region of the Fourier spectrum can be used as an indicator by which to judge the likelihood of occurrence of such phenomena.