A lattice regularization of the supersymmetric Wess-Zumino model is studied by using Ginsparg-Wilson operators. We recognize a certain conflict between the lattice chiral symmetry and the Majorana condition for Yukawa couplings, or in Weyl representation a conflict between the lattice chiral symmetry and Yukawa couplings. This conflict is also related, though not directly, to the fact that the kinetic (Kähler) term and the superpotential term are clearly distinguished in the continuum Wess-Zumino model, whereas these two terms are mixed in the Ginsparg-Wilson operators. We illustrate a case where lattice chiral symmetry together with naive Bose-Fermi symmetry is imposed by preserving a SUSY-like symmetry in the free part of the Lagrangian; one-loop level non-renormalization of the superpotential is then maintained for finite lattice spacing, though the finite parts of wave function renormalization deviate from the supersymmetric value. All these properties hold for the general Ginsparg-Wilson algebra independently of the detailed construction of lattice Dirac operators.