This work studied zinc incorporation into the non-stoichiometric hydroxyapatite (nHAp) and its influence on j potential via investigation on microstructure of synthesised powders. Four hydroxyapatite powders containing zinc cations (2–8 mol.-%) were synthesised via precipitation method. The results showed that zinc cations could not be replaced in calcium vacancies in the sample with 2 mol.-% zinc incorporation. According to the results, substitution of Zn into nHAp occurred completely in the sample with 6 mol.-% of zinc fraction. The calcium vacancies were partially substituted by the zinc cations in the samples containing 4 and 8 mol.-% zinc fraction. The j potential measurements indicated that positive charges were formed in all powders. In addition, the j potential of incorporated samples that Zn2z was displaced from calcium vacancies was higher than others due to formation of extrinsic defect.