Defect levels induced by defect-complexes in Ge play important roles in device fabrication, characterization, and processing. However, only a few defect levels induced by defect-complexes have been studied, hence limiting the knowledge of how to control the activities of numerous unknown defect-complexes in Ge. In this study, hybrid density functional theory calculations of defect-complexes involving oversize atom (indium) and n-type impurity atoms in Ge were performed. The formation energies, defect-complex stability, and electrical characteristics of induced defect levels in Ge were predicted. Under equilibrium conditions, the formation energy of the defect-complexes was predicted to be within the range of 5.90–11.38 eV. The defect-complexes formed by P and In atoms are the most stable defects with binding energy in the range of 3.31-3.33 eV. Defect levels acting as donors were induced in the band gap of the host Ge. Additionally, while shallow defect levels close to the conduction band were strongly induced by the interactions of Sb, P, and As interstitials with dopant (In), the double donors resulting from the interactions between P, As, N, and the host atoms including In atom are deep, leading to recombination centers. The results of this study could be applicable in device characterization, where the interaction of In atom and n-type impurities in Ge is essential. This report is important as it provides a theoretical understanding of the formation and control of donor-related defect-complexes in Ge.