We have succeeded in fabricating a photonic crystal nanocavity with a photon lifetime of 2.1 ns, which corresponds to a quality factor of 2.5 x 10(6). This lifetime is the longest recorded thus far in photonic crystal cavities, and was brought about by improvements in the fabrication process. Comparing our experimental quality factor with the results of calculations shows that we have suppressed variations in the radii and positions of the air holes composing a nanocavity such that their standard deviations are less than 1 nm.