Here is an unusual but common couple found in hotel rooms around Japan, especially in hotels that cater to foreigners. Yes it is a copy of the New Testament in Japanese and English and a copy of the Teaching of Buddha in Japanese and English. The bible was placed by the Gideons, and the Buddhist book placed by some Japanese Buddhist group.
I have stayed at various types of hotels in Japan and from what I have noticed either the books are there together or not at all. There may be cases where it is solely the New Testament or Teachings of Buddha but I have yet to see that.
Hotels that cater mainly to business men are less likely to have these books and much more likely to have the tv remote placed next to the porn channel guide on the desk. Ive stayed at the business type of hotels because they are cheap and clean. For example near Mount Fuji I stayed at a place that had business hotel in the name but lots of budget travellers stayed also. I don’t watch porn but for the Catholic visiting Japan who might be tempted you might want to choose a bit more upscale hotel where the “adult” channel pamphlets aren’t so noticeable, and the New Testament is.