Nanopowders of hydroxyapatite (HA), modified by magnesium (MgHA) and by silicon (SiHA) were obtained by liquid-phase microwave synthesis method. X-ray diffraction and IR spectroscopy results showed that Mg2+ and SiO4 4− ions were present in the synthesized products both as secondary phases and as part of the HA phase. Whitlockite was found in the magnesium-modified HA (MgHA) and larnite was found in the silicon-modified HA (SiHA); ion substitution for both materials resulted in solid solutions. In the synthesized samples of modified HA, the increase of particle size of powders was in the order HA < SiHA < MgHA, which was calculated through data specific surface area and measured pycnometric density of the powders. The Lewis acid sites (Ca2+, Mg2+, Si4+) were present using spectral probes on the surface of the samples of HA, MgHA, and SiHA, and the acidity of these sites decreased in the order SiHA > MgHA > HA. The rates of calcium phosphate layer deposition on the surface of these materials at 37 °C in the model simulated body fluid solution showed similar dependence.