After ruling out medical reasons, I would keep a very close watch on puppy as kitty goes to use litter box. If puppy approaches kitty in box - and worse - interferes, cat will find a new place to go. This applies to bringing in a new cat as well. Think of it, if you were attacked while sitting on the toilet you wouldn't be too happy. When I went through this, I fortunately happened to see my 10 lb. cat squat over half of a honeydew melon on the counter. Good thing I saw it happening. Even if dog is not being overly aggressive, one does like an opportunity to finish one's business. Except for my husband's cat - the 22 lb. monster - who makes sure my Eskimo hears him enter the box.
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