Nanometer-scale defects on the surface of a Si wafer, fabricated by nanoindentation technique, were examined using Raman microscopy and scanning surface potential microscopy to determine the quantitative relation between surface potential shift and Raman shift. Formation of cracks has not observed at the defect sites, indicating that the plastic and elastic deformations were a major issue and that the residual stress from the plastic deformation was observed. The Raman peak of the array of defects formed by nanoindentation shifted to a lower wavenumber as the indentation force was increased. The results indicated that the amount of tensile strain increased with the indentation force, that is, tensile stress was dominant over the condition in the surrounded area, in the indentation-induced defects. Correspondingly, the surface potential of the defect arrays shifted to the negative direction with an increase in indentation force. These results suggest that the tensile stress at the defect site, indicated by the Raman shift, causes the negative shift in the surface potential, which is related to chemical reactivity. Furthermore, Raman shift of a single indent on a silicon-on-insulator (SOI) wafer was observed, which revealed an enhancement in the source-to-noise ratio of the Raman spectrum at the Si defect site, because the ratio of the volume of the defect site to that of the unstrained site increased due to the thin Si layer on the SOI wafer.