Transition-metal atoms with d electrons sometimes form clusters in crystals, which significantly affect the physical properties. Such a cluster formation frequently accompanies a change in the crystal system, leading to the presence of domains with different crystal orientations. In particular, the cubic symmetry is rarely retained after the cluster formation. Here, we identify a cubic-to-cubic phase transition in lacunar spinel GaNb 4 Se 8 , where the change in the lattice parameter is less than 0.0001%. Each Nb 3.25+ tetramer with seven 4d electrons is distorted into an Nb 3+ trimer and an Nb 4+ monomer induced by charge disproportionation among Nb ions. While the Nb 3+ trimer with six 4d electrons forms spin singlets in the σ-bonding orbitals for three Nb−Nb bonds, a localized S = 1/2 spin remains on the Nb 4+ ion. Furthermore, a local electric dipole moment is induced along the 3-fold rotation axis of each distorted tetramer by the cluster rearrangement. The electric dipole moments are regularly arranged to maintain cubic symmetry, giving rise to chiral order.