The defect distribution and Schottky barrier at metal/Ge interfaces were studied using first-principles calculation. It was shown that the defect density markedly increases around the interface owing to the stabilization caused by the hybridization of defect electronic states with metal-induced gap states (MIGS) and by the associated small elastic energy loss around the interface. By comparing the formation energies of various defects at a variety of metal/substrate interfaces, we showed that MIGS not only control the Schottky barrier but also promote a defect-density increase at most metal/semiconductor interfaces. Moreover, we showed that interface oxide layers block MIGS penetration into the Ge substrate and promote the observed breakdown of Fermi-level pinning.