In this article, we study the relations of horizontally homothetic harmonic morphisms with the stability of totally geodesic submanifolds. Let $varphi:(M^n,g) ightarrow(N^m,h)$ be a horizontally homothetic harmonic morphism from a Riemannian manifold into a Riemannian manifold of non-positive sectional curvature and let T be the tensor measuring minimality or totally geodesics of fibers of $varphi$. We prove that if T is parallel and the horizontal distribution is integrable, then for any totally geodesic submanifold P in N, the inverse set, $varphi^{-1}$(P), is volume-stable in M. In case that P is a totally geodesic hypersurface the condition on the curvature can be weakened to Ricci curvature.