A series of experiments have elucidated the primary defects in group-III nitride epilayers, identifying vacancy clusters due to cation migration at interfaces to mitigate strained lattice. While the occurrence of these defects is well-documented, the underlying electronic mechanisms driving vacancy agglomeration in nitrides and their alloys remain poorly understood. In this study, we uncovered a previously unreported ground state of two metal vacancies driven by the migration of kinetically unstable nitrogen atoms using an ab initio approach. Our findings reveal that the mixed covalent-ionic bond character of nitrides is a crucial factor in determining the stability of vacancy clusters. Notably, the relatively strong ionic character of AlN facilitates the formation of exceptionally stable vacancy clusters with a pyramidal nitrogen complex. In contrast, GaN, despite having similar covalent bonding strength, exhibits less stable vacancy clusters due to its weaker ionic character. Moreover, in InN, we observe the formation of molecular-like azide anion that creates a trimer metallic-like bond between indium dangling bonds, accompanied by vigorous indium migration. In the process, we newly identified the formation of a Schottky-Frenkel composite defect. We believe that these novel insights into the bond character and stability of vacancy clusters in nitrides provide a new understanding that could drive the design and optimization of nitride-based materials and electronic devices.