Various calcium phosphate bioceramics are distinguished by their excellent biocompatibility and osteoconductivity. Especially, the exceptional biodegradability of $eta$-TCP makes it a bone graft substitute of choice in many clinical applications. The activation of osteoclasts, differentiated from macrophage precursor cells, trigger a cell-mediated resorption mechanism that renders $eta$-TCP biodegradable. Based on this evidence, we studied the biodegradation process of granular-type $eta$-TCP bone graft substitute through in vitro and in vivo studies. Raw 264.7 cells treated with RANKL and M-CSF differentiated into osteoclasts with macrophage-like properties, as observed with TRAP stain. These osteoclasts were cultured with $eta$-TCP nano powders synthesized by microwave-assisted process. We confirmed the phagocytosis of osteoclasts by observing $eta$-TCP particles in their phagosomes via electron microscopy. No damage to the osteoclasts during phagocytosis was observed, nor did the $eta$-TCP powders show any sign of cytotoxicity. We also observed the histological changes in subcutaneous tissues of rats implanted with granule-type $eta$-TCP synthesized by fibrous monolithic process. The $eta$-TCP bone graft substitute was well surrounded with fibrous tissue, and 4 months after implantation, 60% of its mass had been biodegraded. Also, histological findings via H&E stain showed a higher level of infiltration of lymphocytes as well as macrophages around the granule-type $eta$-TCP. From the results, we have concluded that macrophages play an important role in the biodegradation process of $eta$-TCP bone graft substitutes.