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1 If the liver is unable to break down the ammonia it is excreted in the urine.  Other diseases - Other common causes of the ammonia smell in urine are diabetes, metabolic disorders, sexually transmitted diseases, medications, vitamins, and nutritional supplements.
Neutralizing Pet Ammonia. 1  1. Soak up the urine. Apply layers of paper towels as soon as you discover the urine stain. 2  2. Create a neutralizing mixture. Mix a solution of one part white vinegar to one part water. 3  3. Allow the mixture to settle. Wait 10 minutes.  4. Clear the area. Let the area dry until it is slightly 1  damp. 5. Vacuum the area.