Thin Ge films directly grown on Si substrate using two-step low temperature growth technique are subjected to low load nano-indentation at room temperature. The nano-indentation is carried out using a Berkovich diamond tip (R ~ 20 nm). The residual impressions are studied using ex-situ Raman Micro-Spectroscopy, Atomic Force Microscopy combined system, and Transmission Electron Microscopy. The analysis of residual indentation impressions and displacement-load curves show evidence of deformation by phase transformation at room temperature under a critical pressure ranging from 4.9GPa-8.1GPa. Furthermore, the formation of additional Ge phases such as r8-Ge, hd-Ge, and amorphous Ge as a function of indentation depth have been realized. The inelastic deformation mechanism is found to depend critically on the indentation penetration depth. The non-uniform spatial distribution of the shear stress depends on the indentation depth and plays a crucial role in determining which phase is formed. Similarly, nano-indentation fracture response depends on indentation penetration depth. This opens the potential of tuning the contact response of Ge and other semiconductors thin films by varying indentation depth and indenter geometry. Furthermore, this observed effect can be reliably used to induce phase transformation in Ge-on-Si with technological interest as a narrow band gap material for mid-wavelength infrared detection.