The oxidation states formed during low-temperature oxidation (T < 500 K) of a Ru(0001) surface are identified with photoelectron spectromicroscopy and thermal desorption (TD) spectroscopy. Adsorption and consecutive incorporation of oxygen are studied following the distinct chemical shifts of the Ru 3d(5/2) core levels of the two topmost Ru layers. The evolution of the Ru 3d(5/2) spectra with oxygen exposure at 475 K and the corresponding O2 desorption spectra reveal that about 2 ML of oxygen incorporate into the subsurface region, residing between the first and second Ru layer. Our results suggest that the subsurface oxygen binds to the first and second layer Ru atoms, yielding a metastable surface "oxide", which represents the oxidation state of an atomically well ordered Ru(0001) surface under low-temperature oxidation conditions. Accumulation of more than 3 ML of oxygen is possible via defect-promoted penetration below the second layer when the initial Ru(0001) surface is disordered. Despite its higher capacity for oxygen accumulation, also the disordered Ru surface does not show features characteristic for the crystalline RuO2 islands. Development of lateral heterogeneity in the oxygen concentration is evidenced by the Ru 3d(5/2) images and microspot spectra after the onset of oxygen incorporation, which becomes very pronounced when the oxidation is carried out at T > 550 K. This is attributed to facilitated O incorporation and oxide nucleation in microregions with a high density of defects.