TOKYO—After 79 days in jail, it was pain from sitting too long that finally made Masamichi Sakai confess to a crime he says he didn’t commit.

The 63-year-old owner of a construction company, under wardens’ orders, couldn’t stand or lie down in his cell. Pressure sores on his skin burned, he missed his family—which was barred from visiting him—and his own lawyer was telling him to admit everything.

Mr….

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