The functional properties of Mn-doped Ge depend to large extent on the lattice location of the Mn impurities. Here, we present a lattice location study of implanted diluted Mn by means of electron emission channeling. Surprisingly, in addition to the expected substitutional lattice position, a large fraction of the Mn impurities occupies the bond-centered site. Corroborated by ab initio calculations, the bond-centered Mn is related to Mn-vacancy complexes. These unexpected results call for a reassessment of the theoretical studies on the electrical and magnetic behavior of Mn-doped Ge, hereby including the possible role of Mn-vacancy complexes.