A lattice QCD calculation of the kaon $B$ parameter $B_K$ is carried out with the Wilson quark action in the quenched approximation at $beta=6/g^2=5.9-6.5$. The mixing problem of the $Delta s=2$ four-quark operators is solved non-perturbatively with full use of chiral Ward identities employing four external quarks with an equal off-shell momentum in the Landau gauge. This method, without invoking any effective theory, enables us to construct the weak four-quark operators exhibiting good chiral behavior. Our results for $B_K$ with the non-perturbative mixing coefficients show small scaling violation beyond the lattice cut-off $a^{-1}sim 2.5 $GeV. Our estimate concludes $B_K(NDR, 2 GeV)=0.69(7)$ at $a^{-1}=2.7-4.3$GeV, which agrees with the value obtained with the Kogut-Susskind quark action. For comparison we also calculate $B_K$ with one-loop perturbative mixing coefficients. While this yields incorrect values at finite lattice spacing, a linear extrapolation to the continuum limit as a function of $a$ leads to a result consistent with those obtained with the Ward identity method.