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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.
The Test Sample. Ammonia is a waste product formed primarily by bacteria in the intestines during the digestion of protein. If not processed and cleared from the body appropriately, excess ammonia can accumulate in the blood. This test measures the amount of ammonia in the blood. Ammonia is normally transported in the blood to the liver, where it is converted into two substances called urea and glutamine. The urea is then carried to the kidneys, where it is eliminated in the urine.