We present our result for the $K\to\pi\pi$ decay amplitudes for both the $\Delta I=1/2$ and $3/2$ processes with the improved Wilson fermion action. Expanding on the earlier works by Bernard {\it et al.} and by Donini {\it et al.}, we show that mixings with four-fermion operators with wrong chirality are absent even for the Wilson fermion action for the parity odd process in both channels due to CPS symmetry. Therefore, after subtraction of an effect from the lower dimensional operator, a calculation of the decay amplitudes is possible without complications from operators with wrong chirality, as for the case with chirally symmetric lattice actions. As a first step to verify the possibility of calculations with the Wilson fermion action, we consider the decay amplitudes at an unphysical quark mass $m_K \sim 2 m_\pi$. Our calculations are carried out with $N_f=2+1$ gauge configurations generated with the Iwasaki gauge action and nonperturbatively $O(a)$-improved Wilson fermion action at $a=0.091\,{\rm fm}$, $m_\pi=280\,{\rm MeV}$, and $m_K=580\,{\rm MeV}$ on a $32^3\times 64$ ($La=2.9\,{\rm fm}$) lattice. For the quark loops in the penguin and disconnected contributions in the $I=0$ channel, the combined hopping parameter expansion and truncated solver method work very well for variance reduction. We obtain, for the first time with a Wilson-type fermion action, that ${\rm Re}A_0 = 60(36) \times10^{ -8}\,{\rm GeV}$ and ${\rm Im}A_0 =-67(56) \times10^{-12}\,{\rm GeV}$ for a matching scale $q^* =1/a$. The dependence on the matching scale $q^*$ for these values is weak.
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