Sputter etching (SE) of Si substrate is employed to fabricate highly-oriented β-FeSi2 film on Si by means of ion beam sputter deposition (IBSD). In the present study, dependence on the irradiated fluence at the incident SE energies of 1 and 3 keV and at the deposition temperatures of 923 and 973 K, was investigated to discuss whether it is possible to obtain highly-oriented β-FeSi2 thin film with less radiation damage. At 973 K, irradiation of 3 keV Ne+ to an ion fluence of 3.7×1016 Ne/cm2 was needed to avoid the formation of α-FeSi2 phase and to obtain highly-oriented β-FeSi2 (100) film on Si (100) substrate. Whereas at 923 K highly-oriented β-FeSi2 (100) film was obtained with SE condition of 3 keV and 3.7×1015 Ne/cm2, which is merely 1/10 of the fluence required at 973 K. This means that the β-FeSi2 film can be fabricated with much less radiation damage so that presence of defects is considered to be much reduced.