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We propose a new possibility to realize simultaneously the sufficient protonstability and the interesting structure of neutrino mass matrix in superstringinspired $E_6$ models. In this model the leptons and Higgs fields are assignedto a fundamental representation {\bf 27} in the different way amonggenerations. Two pairs of Higgs doublets naturally remain light from threegeneration ones by imposing certain discrete symmetries, although all extracolor triplets become sufficiently heavy. Under these symmetries suitable$\mu$-terms to bring appropriate vacuum expectation values are prepared and thedangerous FCNC is avoidable. Some related phenomena to this model, especially,the structure of neutrino mass matrix are also discussed.Comment: 20 pages, latex, a version published in Prog. Theor. Phys.,  discussions related to neutrino masses are change

Proton Stability and Small Neutrino Mass in String Inspired E6 Models