Raman measurements were investigated on Zr-doped lithium niobate LiNbO3 crystals with different concentrations. Spectra were treated by fitting procedure and principal component analysis which both provide results consistent with each other. The concentration dependence of the frequency on the main low-frequency optical phonons provides an insight of site incorporation of Zr ions in the host lattice. The threshold concentration of about 2% is evidenced, confirming the interest of Zr doping as an alternative to Mg doping for the reduction of the optical damage in lithium niobate.