That would require an understanding of Japan's judiciary system, but I'm going to presume it's because of the same reason why death sentences take so long to carry out in the U.S. Presumption of innocence, due process, and the right to appeal. The alleged has every right to appeal their case and this process takes time to re-examine evidence and this can go through multiple courts before they exhaust all legal options. Terminating a life is not a decision to be made lightly.
Which is why, contrary to popular belief, it's cheaper to keep someone alive than to sentence them to death.