A method for controlling reductant injection into an exhaust stream upstream of a catalyst coupled to an internal combustion engine is disclosed. In the method, an ammonia sensor located downstream of the exhaust catalyst is used to determine ammonia concentration in the exhaust stream. The ammonia concentration is compared to an allowable threshold and an allowable fraction, i.e., a maximum limit on a fraction of ammonia in the exhaust stream compared with the ammonia supplied by the reductant injector. Additionally, based on a NOx sensor, it is determined whether NOx conversion of the catalyst has increased in response to an increase in reductant injection. If not, reductant injection quantity is reduced.