- Agriculture Department
- Arts and Culture Department
- Manipur State Archives Department
- Command Area Development Authority (CADA) Department
- Co-operation Department
- Commerce and Industries Department
- Consumer Affairs, Food and Public Distribution Department
- Development of ST & SC Department
- Economics & Statistics Department
- Education (S) Department
- Education (U) Department
- Election Department
- Finance Department
- Directorate of Treasuries and Account Department
- Directorate of Institutional Finance Department
- Directorate of MIS Department
- Taxation Department
- Finance Commission Department
- GAD Department
- Printing and Stationery Department
- Fisheries Department
- Forest and Environment Department
- Ecology and Environment Department
- Forest Department
- Horticulture and Soil Conservation Department
- Home Department
- Manipur Police Department
- Manipur Rifles Department
- Home Guards Department
- CMTW Department
- MPTC Department
- Forensic Science Laboratory Department
- Manipur Police Housing Corporation Department
- Manipur Traffic Police Department
- Narcotics & Affairs of Border Department
- Imphal Municipal Corporation (IMC) Department
- Irrigation and Flood Control (IFCD) Department
- Information Technology Department
- Information and Public Relations Department
- Labour Department
- Employment Exchange Department
- Law and Legislative Affairs Department
- MAHUD Department
- Manipur Development Society Department
- Manipur Urban Development Agency (MUDA) Department
- Medical & Health Service Department
- National Rural Health Mission Department
- Minor Irrigation Department
- Minorities and Other Backward Classes Department
- Personnel and Administrative Reforms Department
- Planning Department
- Power Department
- Manipur State Designated Agency Department
- Public Health Engineering Department
- Public Works Department
- Relief and Disaster Management Department
- Revenue Department
- Directorate of Settlement & Land Record Department
- Rural Development and Panchayati Raj Department
- Science and Technology Department
- MANIREDA Department
- MASTEC Department
- Sericulture Department
- Social Welfare Department
- Disability Department
- State Academy of Training(SAT) Department
- Town Planning Department
- Tourism Department
- Sangai Festival Department
- Veterinary and Animal Husbandry Department
- Vigilance Department
- Youth Affairs and Sports Department