The conventional method using low energy theorems  does not seem to lead to an explicit unitarity limit in the scattering processes of longitudinally polarized gauge bosons for the high energy case in the extra U(1) superstring inspired models, commonly known as eta model, emanating from E6 group of superstring theory. We have made use of an alternative procedure given in , which is applicable to SUSY GUT. Explicit unitarity bounds on the Yukawa couplings are obtained from both using unitarity constraints as well as using RGE analysis at one-loop level utilizing critical couplings concepts implying divergence of scalar coupling at MG. These are found to be consistent with finiteness over the entire range MZ<=sqrt(s)<=MG. For completeness, the similar approach has been made use of in other models, i.e., chi, psi, and nu models emanating from E6 and it has been noticed that at weak scale, the unitarity bounds on Yukawa couplings do not differ among E6 extra U(1) models significantly except for the case of chi model in 16 representations. Theoretically we have obtained the upper bounds on top quark and lightest neutral higgs boson mass using the unitarity constrained superpotential couplings and also obtained the D-quark mass as a function of MZ2 is O(3 TeV) for MZ2 is O(1 TeV). The obtained bounds on these physical parameters are found consistent with the present day experimental precision measurements.