Here, we report on the increase of the quality-factors of photonic crystal nanocavities fabricated by a CMOS-compatible process. We fabricated nanocavities with the same cavity design but used either a binary photomask or a phase-shift photomask in the photolithography step to assess the impact of the photomask-type on the fabrication accuracy of the air holes. We characterized 62 cavities using time-resolved measurements and the best cavity had a quality-factor of 6.65 × 106. All cavities exhibited a quality-factor larger than 2 million and the overall average was 3.25 × 106. While the estimated magnitude of the scattering loss due to the air hole variations in the 33 cavities fabricated with the phase-shift photomask was slightly lower than that in the 29 cavities fabricated with binary photomask, the phase-shift photomask did not provide a significant improvement in the fabrication accuracy. On average, the scattering loss in these samples is more than 3 times larger than that of nanocavities fabricated using electron-beam lithography, which indicates room for further improvement.