Strong interactions preserve an approximate isospin symmetry between up (u) and down (d) quarks, part of the more general flavor symmetry. In the case of K meson production, if this isospin symmetry were exact, it would result in equal numbers of charged (K+ and K−) and neutral (K0 and $${\overline{K}}^{0}$$) mesons produced in collisions of isospin-symmetric atomic nuclei. Here, we report results on the relative abundance of charged over neutral K meson production in argon and scandium nuclei collisions at a center-of-mass energy of 11.9 GeV per nucleon pair. We find that the production of K+ and K− mesons at mid-rapidity is (18.4 ± 6.1)% higher than that of the neutral K mesons. Although with large uncertainties, earlier data on nucleus-nucleus collisions in the collision center-of-mass energy range $$2.6 \, < \, \sqrt{{s}_{NN}} \, < \, 200$$GeV are consistent with the present result. Using well-established models for hadron production, we demonstrate that known isospin-symmetry breaking effects and the initial nuclei containing more neutrons than protons lead only to a small (few percent) deviation of the charged-to-neutral kaon ratio from unity at high energies. Thus, they cannot explain the measurements. The significance of the flavor-symmetry violation beyond the known effects is 4.7σ when the compilation of world data with uncertainties quoted by the experiments is used. New systematic, high-precision measurements and theoretical efforts are needed to establish the origin of the observed large isospin-symmetry breaking.