Calcium phosphate (CAP) has a wide range of applications in biomedical systems. Although there is great potential for the use of CAP in the development of gene delivery systems, the uncontrollable growth of CAP crystal makes it difficult to use in a practical nano-gene delivery system. The purpose of this study was to develop nano-sized CAP particles containing nucleic acids (e.g. DNA, siRNA). The CAP nano-aggregates (CAP/pDNA/dopa-Chi) were successfully prepared by serial addition of plasmid DNA (pDNA) and dopa (3,4-dihydroxy-l-phenylalanine) modified chitosan to growing CAP particles in calcium phosphate solution. The addition of the dopa moiety is thought to enable chitosan adsorption onto the surface of forming calcium phosphate particles to prevent further growth. The CAP/pDNA/dopa-Chi significantly increased the serum stability of pDNA, and showed high cellular uptake efficiency and trans-gene expression. Additionally, the chitosan stabilized CAP nano-aggregates were also prepared for siRNA delivery (CAP/siRNA/dopa-Chi) via the same method as for CAP/pDNA/dopa-Chi. A notable siRNA gene silencing effect of CAP/siRNA/dopa-Chi was exhibited without any sign of cytotoxicity.