In the present report, the structural stability order and electronic properties of the transition metal M@Ge12 (M = Co, Pd, Tc, and Zr) doped germanium cage has been carried out at B3LYP/LANL2DZ ECP level by using spin polarized density functional theory. Initially, we selected five lowest energy structure of neutral TM doped Ge12 cluster with high symmetry point like D6h-symmetric hexagonal prism (HP), the D6d-symmetric hexagonal anti-prism (HAP), D2d-symmetric bi-capped pentagonal prism (BPP), perfect icosahedrons (Ih) and Fullerene type structures. Further, we discussed the electronic origin of stability as well as electronic properties by calculating binding energy, HOMO-LUMO gap, charge transfer mechanism and density of states. We indentified that the Pd, Tc, and Zr encapsulated Ge12 cage with hexagonal prism [HP] structures are minimum energy structures while Co@Ge12 cage prefer HAP structure. The magnitudes of binding energy of the clusters indicate that the doping of 4d transition metal gives most stable structure rather than 3d transition metal Co atom. The large HOMO-LUMO gap and natural bond orbital analysis explain the stability of these clusters using closed shell electronic configuration and the contribution of π and σ bond. Charge transfer mechanism shows that the Tc, Pd and Zr atoms play role as an electron donor in the system whereas Co inclined to accept the electrons. The importances of “d” orbital in localized electrons near the Fermi level are also explained through partial density of states.