A radio-frequency magnetron sputtering technique operating in right-angle geometry (RAMS) with high plasma confinement was revised to produce thin films (15-570nm) of fluorine-substituted hydroxyapatite, FHA, adapted to be used as nano-coatings for biomedical implants. An electron temperature of Teff≈9.0eV and a plasma electron density of 1.2×1015m-3 assured the nucleation of an amorphous fluorine-substituted hydroxyapatite phase on Si and Ti surfaces. With the aid of a Langmuir probe, the RAMS plasma energy was tuned to control the coating stoichiometry and the ratio between the crystalline and amorphous phases. The energy delivered over time from the bombardment of ions and electrons transformed the amorphous calcium phosphate phase into crystalline fluorine-substituted hydroxyapatite. The crystalline films were obtained at room temperature. The partial substitution of OH- for F- in the HA structure was confirmed by X-ray diffraction using synchrotron radiation in grazing-incidence mode, X-ray photoelectron spectroscopy and attenuated total reflection Fourier transform infrared spectroscopy. High-resolution transmission electron microscopy carried out on cross-section film samples prepared by a focused ion beam (FIB) technique revealed that the film ultrastructure was composed of columnar crystals oriented perpendicularly to the substrate surface. The crystals were connected to the substrate surface by ordered nanolayers, indicating the existence of a continuous binding between the two materials. This work demonstrates that the RAMS technique is able to produce FHA nano-coatings with controlled chemical compositions and structures on metallic implants for clinical applications.