To protect the coastal areas of the seas and oceans from the destructive force of tsunami waves, coastal and surface barriers are usually built. However, for high waves, these barriers turn into underwater barriers through which tsunami waves pass practically without losing their energy. In this paper, we study a new principle of suppression of the energy of tsunami waves by underwater barriers. The problems of experimental and numerical modeling of the processes of generation, propagation, and interaction of gravity wave of the tsunami type with underwater barriers are considered. It is shown that, under certain conditions near the underwater barriers, large-scale vortex structures occur that accumulate a significant part of the energy of the incident wave. Here, if the barriers parameter h/(H + A) = 0.84 ÷ 0.85 (h—height of the barriers, A—amplitude of incident wave on a barrier, H—depth of the reservoir), then the vortex structures accumulate up to 50% of the wave energy incident on the barrier. A theoretical model explaining the effect of anomalous vortex suppression of tsunami wave energy by underwater barriers has been developed. Theoretical calculations and results of numerical modeling based on the Navier–Stokes Equations are consistent with experimental studies in a hydrodynamic wave flume.