At high energies the saturation effects associated to the high parton density should modify the behavior of the observables in proton-nucleus and nucleus-nucleus scattering. In this paper we investigate the saturation effects in the nuclear J/Ψ production and estimate the modifications in the energy dependence of the cross section as well as in the length of the nuclear medium. In particular, we calculate the ratio of J/Ψ to Drell-Yan cross sections and show that it is strongly modified if the high density effects are included. Moreover, our results are compared with the data from the NA50 Collaboration and predictions for the RHIC and LHC kinematic regions are presented. We predict an additional J/Ψ suppression associated to the high density effects.