The ammonia removal ability of heterotrophic bacteria Alcaligenes faecalis strain No.4 isolated from sewage sludge was examined in a batch operation to mitigate ammonia from piggery wastewater, consequently preventing pollution by the inflow of wastewater from piggeries adjacent to rivers. If this process works functionally, it can be effective in controlling nitrous oxide (N2O) and nitrate (NO3−) emissions derived from animal agriculture, the heterotrophic nitrifying and the aerobic denitrifying effect of A. faecalis strain No.4 on high-strength ammonium (NH4+-N) were evaluated in wastewater collected from a piggery. The removal rate by A. faecalis strain No.4 on high-strength ammonium (NH4+-N) was 0.97 kg N/m3/day which was more than 100 fold greater than that achieved using conventional aerobic nitrification and anaerobic denitrification processes. An aerobic one-step denitrification system using A. faecalis strain No.4 can be proposed to remove ammonia and phytopathogens from piggery wastewater with high efficiency and prevent water pollution in adjacent rivers.