The refractive-index profiles induced by high-energy (5 MeV, 7.5 MeV) silicon irradiation in LiNbO$3$ have been systematically determined as a function of ion fluence in the range $10^{13}$–$10^{15}$ cm$^{-2}$. At variance with irradiations at lower energies, an optically isotropic (‘amorphous’) homogeneous surface layer is generated whose thickness increases with fluence. These results have been associated with an electronic excitation mechanism. They are discussed in relation to the well-documented phenomenon of latent (amorphous) track generation under ion irradiation, requiring a threshold value $S{e,\textrm{th}}$ for the electronic stopping power $S_e$. Our optical data have yielded a value of ≈5 keV/nm for such a threshold, within the range reported by independent single-track measurements. The propagation of the amorphous boundary into the crystal during irradiation indicates that the threshold value decreases on increasing the fluence. Complementary Rutherford backscattering–channeling and micro-Raman (on samples irradiated at 30 MeV) experiments have been performed to monitor the induced structural changes.