Self-supplying forage might be a possible source of the infection of Mycobacterium avium subsp. paratuberculosis (MAP) in a farm where paratuberculosis has been diagnosed. We investigated the effects of ammonia treatment under various conditions on the viability of MAP inoculated in low moisture roughage. One hundred gm of ground alfalfa hay was put into a resin bag(180x240mm), and was used as a container for ammonia treatment. Ammonia treatment on a laboratory scale was performed by adding NH4OH and a filter paper containing inoculum into it before sealing. The viability of MAP was decreased in conditions more advantageous to chemical reactions that promote high concentration, high temperature, and a prolonged high moisture treatment period. However, by the addition of 1 and 2% concentrations of ammonia treatment, MAP was observed to survive under low temperature and low moisture conditions, with its number decreasing under conditions in which material moisture or temperature was kept higher than it. At a 3% concentration, except for the 1st day of 10 and 20% moisture conditions, since any survivor of it was not observed. Since weak correlation coefficients between viability and material moisture, processing temperature, ammonia concentration, the number of treatment dates were determined as -0.39, -0.38, -0.34, and -0.26, respectively, the following methods are for reducing the viability rate are presented in the descending order of their effectiveness: adding water to material > increasing of processing temperature > increasing of ammonia concentration > extension of processing period.