In the present investigation, nano hydroxyapatite (HAp) and fluorine substituted hydroxyapatite (FHAp) with varying fluorine concentrations have been successfully prepared by hydrothermal method. The as synthesized powders were characterized using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), high resolution transmission electron microscope (HRTEM) and ion chromatography (IC) for fluorine content analysis. XRD results showed shifting of HAp peaks with increasing fluorine substitution and detected calcium fluoride (CaF2) phase in the synthesized powders where theoretically 100% or more OH ions substituted by F ions. The crystallinity of HAp powder gradually increased and cell volume decreased with fluorine substitution. HRTEM of the synthesized powders showed the nano rod like morphology. The IC was carried out to understand the degree fluoridation in the synthesized powder. The IC result of in vitro fluorine ion leaching showed that fluorine concentration in aqueous medium depends on the degree of fluoridation in the synthesized powder. The as synthesized powders were checked for antimicrobial activity by using both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) strains. The powder having ~33% fluorine substitution showed bactericidal effect. The in vitro fluorine ion release study showed significantly high fluorine concentration in aqueous medium for the HAp powders having more than 50% fluorine substituted. The in vitro cell viability assay using mouse osteoblast cell line (MC3T3-E1) confirmed that the powders were non-cytotoxic.