The estimated enteric methane EFs for adult males used for breeding & for other purposes, adult multipurpose cows, adult males used for draught, growing males, growing females, calves aged 6monts-1 year (male and female) and calves aged < 6 months (male and female) were significantly (P < 0.01) different than those of cattle subcategories. The estimated enteric CH 4 EF of dual-purpose cattle were significantly (P < 0.001) differed between lowland agro-ecology and other agro-ecologies. Among the total population in the zone, cattle (accounted 83.88%) of the total population. Among the agro-ecologies, the lowland area had the highest share (33.61%), followed by the midland (33.23%) and highland (33.16%) areas. The share of agro-ecologies per total population was highland area (43.54%) followed by midland (35.23%) and lowland (21.23%). The estimated CH4 emission from manure handling practices in the study area were significantly different (P < 0.001) between the sub-category of dual-purpose cattle except for those from adult multipurpose cows > 3 years old and those from adult males used for draught (3–10 years old). The estimated CH4 emissions from manure of dual-purpose cattle were significantly (P < 0.001) different between lowland agro-ecology and other agro-ecologies. The estimated nitrous oxide concentrations for adult males used for breeding and other purpose, adult males used for draught, adult multipurpose cows, growing males, growing females, calves aged 6 month–<1 year (male and female) and calves aged < 6 months (male and female) were significantly (P < 0.001) different between the cattle subcategories. The estimated nitrous oxide concentration in dual-purpose cattle were significantly (P < 0.001) greater for lowland agro-ecology than for other agro-ecologies.