Fluorine-doped hydroxyapatite (FHA) and calcium deficient hydroxyapatite (CDHA) were coated on the surface of biodegradable magnesium alloy using electrochemical deposition (ED) technique. Coating characterization was investigated by X-ray diffraction (XRD), Fourier-transformed infrared spectroscopy (FTIR), transmission electron microscopy (TEM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The result shows that nano-FHA coated sample presents nano needle-like structure, which is oriented perpendicular to the surface of the substrate with denser and more uniform layers compared to the nano-CDHA coated sample. The nano-FHA coating shows smaller crystallite size (65 nm) compared to the nano-CDHA coating (95 nm); however, CDHA presents thicker layer (19 μm in thickness) compared to the nano-FHA (15 μm in thickness). The corrosion behaviour determined by polarization, immersion and hydrogen evolution tests indicates that the nano-FHA and nano-CDHA coatings significantly decrease corrosion rate and induce passivation. The nano-FHA and nano-CDHA coatings can accelerate the formation of bone-like apatite layer and significantly decrease the dissolution rate as compared to the uncoated Mg alloy. The nano-FHA coating provides effective protection to Mg alloy and presents the highest corrosion resistance. Therefore, the nano-FHA coating on Mg alloy is suggested as a great candidate for orthopaedic applications.