if u are a non-muslim, you may go to JPN and tell them that you follow no religion and fill up a form. The counter staff will take the form for approval by a superior, and they will duly update the info on your IC chip. In the past (before the IC version with big and small photo), such cases would be just a blank in the religion part of the IC data. I dunno how atheists are designated in the new IC with big and small photo.