We have precisely measured the Raman shift of photonic crystal silicon heterostructure nanocavities for Raman laser applications. We utilized a near-infrared excitation laser of wavelength 1.42 μm in order to avoid local sample heating and exploited two high-Q nanocavity modes to calibrate the Raman frequency. The measured Raman shift was 15.606 THz (520.71 cm(-1)) with a small uncertainty of 1.0 × 10(-3) THz. In addition, we investigated the compressive stress generated in a photonic crystal slab in which a ~5.1 × 10(-3) THz blue shift of the Raman peak and a slight warpage of the slab were observed. We also demonstrated that the stress could be eliminated by using a cantilever structure.