In this study, a mechanochemical method was applied to the synthesis of hydroxyapatite with double and triple substitution. Simultaneous replacement of phosphate ions by carbonate and silicate ions was implemented in the case of double substitution. The triple substitution involved additional replacement of a calcium ion by a zinc ion. The synthesized materials were characterized by X-ray diffraction and Fourier transform infrared spectroscopy. Samples of co-substituted hydroxyapatites in powder form were evaluated in vitro using human osteoblast cell line MG-63 and in vivo via implantation into a bone defect in the rat cranial vault. After 4 days of incubation in vitro, the hydroxyapatite containing zinc, silicon, and carbonate ions with composition Ca9.9Zn0.1(PO4)5.6(SiO4)0.2(CO3)0.2(OH)2 significantly increased cell proliferation in comparison with the other compositions. Four months after the implantation in vivo, this sample showed the greatest ability to integrate into rat skull bones, as evidenced by a morphological analysis of bone sections.