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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.
Causes. Urine odor is related to the volume and concentration of a variety of substances excreted by the kidneys. Normally, urine that contains a lot of water has little to no odor. If your urine becomes highly concentrated â a high level of waste products with little water â urine odor may have a strong ammonia smell. Many foods and medications, such as asparagus or certain vitamins, can affect the odor of urine. Sometimes, unusual urine odor may indicate a medical condition or disease, such as: 1  Bladder infection. 2  Cystitis (bladder inflammation). 3  Dehydration. 4  Diabetic ketoacidosis (high levels of blood acids called ketones). 5  Gastrointestinal-bladder fistula (abnormal connection between the intestines and bladder).