A new nanometrology spectroscopic rapid test technique was developed for the determination of the small carbonate impurity content (0.03%–3%) in the structure of biomimetic nanocomposite materials based on non-stoichiometric nanocrystalline hydroxyapatite. The obtained gage function with high correlation (R2 = 0.98) could be used as an instrument for estimation of the structural changes in bio-apatite materials with a high degree of accuracy.