In this paper, we investigate the embryonic stage of oxidation of an epi Ge(001)-2 × 1 by atomic oxygen and molecular O2 via synchrotron radiation photoemission. The topmost buckled surface with the up- and down-dimer atoms, and the first subsurface layer behaves distinctly from the bulk by exhibiting surface core-level shifts in the Ge 3d core-level spectrum. The O2 molecules become dissociated upon reaching the epi Ge(001)-2 × 1 surface. One of the O atoms removes the up-dimer atom and the other bonds with the underneath Ge atom in the subsurface layer. Atomic oxygen preferentially adsorbed on the epi Ge(001)-2 ×1 in between the up-dimer atoms and the underneath subsurface atoms, without affecting the down-dimer atoms. The electronic environment of the O-affiliated Ge up-dimer atoms becomes similar to that of the down-dimer atoms. They both exhibit an enrichment in charge, where the subsurface of the Ge layer is maintained in a charge-deficient state. The dipole moment that was originally generated in the buckled reconstruction no longer exists, thereby resulting in a decrease in the ionization potential. The down-dimer Ge atoms and the back-bonded subsurface atoms remain inert to atomic O and molecular O2, which might account for the low reliability in the Ge-related metal-oxide-semiconductor (MOS) devices.