In a previous study, natural hydroxyapatite (HAp) from the bones of Brazilian river fish was calcined at 900 °C (4–12 h), and optical characterization using the near infrared photoacoustic spectroscopy technique enabled the establishment of 8 h as the best calcination time for nanostructure stabilization when milled in a high-energy milling device [T. M. Coelho, E. S. Nogueira, W. R. Weinand, W. M. Lima, A. Steimacher, A. N. Medina, M. L. Baesso, and A. C. Bento, J. Appl. Phys. 100, 094312 (2006)]. The fish wastes used were from species such as pintado (Pseudoplatystoma corruscans), jaú (Paulicea lutkeni), and cachara (Pseudoplatystoma fasciatum). In this study, the characterization of the thermal properties of the same natural HAp is discussed for samples milled from 0 to 32 h, with nanostructures from 80 to 24 nm. The powders were pressed into disks at 350 MPa and sintered for 4 h at 1000 °C . Thermophysical parameters were obtained by thermal wave interferometry and nonadiabatic relaxation calorimetry. Results for thermal diffusivity and thermal conductivity showed that the parameters increase with milling time, although they present a transition (a plateau) in the interval from 8 to 16 h. Two different slopes were observed and this was interpreted as being due to the size of the crystallites, which fall rapidly, dropping from 80 nm to near 22 nm when milling time is increased from 0 to 16 h, and forming agglomerates up to 32 h.