Molecular farming is a promising method for producing materials of commercial interest. Plants can be expected to be appropriate hosts for recombinant protein production. However, production in genetically modified plants has two major challenges that must be resolved before its practical use: insufficient accumulation of products and difficulty in establishing methods for their purification. We propose a simple procedure for the production of a desired protein using watery rice seeds lacking an accumulation of storage starch and proteins, a phenotype induced by the introduction of an antisense SPK. We produced a transgenic rice plant containing a gene for an antimicrobial peptide, thanatin, together with antisense SPK. Bioassay and proteome analysis indicated that recombinant thanatin accumulated in an active form in these watery rice seeds. These results suggest that our system worked effectively for the production of thanatin. This procedure enabled easy removal of impurities and simplified the purification process compared with production in leaves. Our system may therefore be a useful technique for the production of desired materials, including proteins.