In this study, the impact of chitosan (CS) on Mg²⁺ incorporation into hydroxyapatite (HAp) was investigated. Initial Mg/(Ca+Mg) ratios of 0–0.15 resulted in Mg-incorporated HAp containing CS (CMgHAp), while a ratio of 0.2 yielded amorphous calcium phosphate containing CS. Mg/(Ca+Mg) and (Ca+Mg)/P molar ratios of the obtained CMgHAp particles were lower than those of Mg-incorporated HAp particles without CS, suggesting that Mg incorporation into HAp was suppressed by CS. Initial Mg/(Ca+Mg) ratio of 0.025 led to CMgHAp particles with lower specific surface area than HAp particles containing CS, while ratios of 0.05–0.15 led to particles with higher specific surface area. Transmission electron microscopy showed aggregated particles of CMgHAp, since the observed particle sizes were larger than the crystallite sizes of CMgHAp calculated using X-ray diffraction patterns. Analyses of Fourier transform infrared spectroscopy confirms the interaction of CS with the phosphate group in Mg-incorporated HAp. Calcination of the CMgHAp particles decreased the particle size and increased the specific surface area due to decomposition of CS, indicating that CS aggregated Mg-incorporated HAp particles.