Systematic analysis of the energy level schemes, ground state absorption (GSA) and covalency effects for the Ni 2+ ion in Ca 3 Sc 2 Ge 3 O 12 was performed. The recently developed first-principles approach to the analysis of the absorption spectra of impurity ions in crystals based on the discrete variational multi-electron method (DV-ME) [K. Ogasawara et al., Phys. Rev. B 64, 115413 (2001)] was used in the calculations. As a result, complete energy level schemes of Ni 2+ and its absorption spectra at both possible crystallographic positions (distorted octahedral Sc 3+ and tetrahedral Ge 4+ positions) were calculated, assigned and compared with experimental data. Energies of the charge transfer (CT) transitions for both positions are estimated. Numerical contributions of all possible electron configurations into the calculated energy states were determined. By performing analysis of the molecular orbitals (MO) population, it was shown that the covalency of the chemical bonds between the Ni 2+ and O 2-ions increases in passing from the hexa-to the tetra-coordinated complex.