Application of hydroxyapatite (HAp) nanoparticles to repair damaged enamel has attracted recent attention. In this study, HAp nanoparticles with various morphologies (spherical, short-rod, long-rod and fiber morphologies) were synthesized via chemical precipitation methods without the addition of template molecules, and the adsorption/desorption behaviors of a cationic antibacterial agent, cetylpyridinium chloride (CPC), on the HAp nanoparticles were evaluated. The adsorption of CPC on each HAp nanoparticle showed Langmuir-type adsorption, and the short-rod/long-rod HAp nanoparticles showed thermodynamically more stable adsorption of CPC than that with the spherical/fiber HAp nanoparticles. The desorption rate of CPC from the short-rod/long-rod HAp nanoparticles was slower than that of the spherical/fiber HAp nanoparticles. The HAp nanoparticles with different CPC release profiles presented here have potential applications as nanoparticulate enamel repair agents with antibacterial properties.