This work reports on the role of carbonate substitution on the mechanical properties of calcium deficient carbonate apatite which resembles closely the structure of bone apatite. The carbonate content determined using vibrational spectroscopy suggests two stage substitutions. The residual stress is evaluated using non-destructive X-ray diffraction procedure for these polycrystalline aggregates. The crystallinity increases with deposition time and increased carbonate substitution does not impede the crystal growth and no phase change is observed. A carbonate content of 6.34wt. % corresponds to a minimum residual stress without compromising the crystallinity of the films. The carbonate substitution might be associated with the calcium vacancy which is considered as the thermodynamically feasible mechanism for B-type carbonate apatite.