| Organization | Department & Ministry | Institution Type | State |
|---|---|---|---|
| National Institute of High Security Animal Diseases (NIHSAD) | Ministry of Agriculture and Farmers Welfare (MoAFW) | — | Madhya Pradesh |
| National Institute of Homoeopathy (NIH) | Ministry of AYUSH | — | West Bengal |
| National Institute of Hydrology (NIH) | Ministry of Jal Shakti | — | Uttarakhand |
| National Institute of Immunohaematology (NIIH) | Ministry of Health and Family Welfare (MoHFW) | — | Maharashtra |
| National Institute of Immunohaemotology (NIIH), Mumbai | Ministry of Health and Family Welfare (MoHFW) | Research Institutions | Maharashtra |
| National Institute of Immunology (NII) | Ministry of Science & Technology (MoST) | Research Institutions | Delhi |
| National Institute of Indian Medical Heritage (NIIMH) | Ministry of AYUSH | — | Telangana |
| National Institute of Malaria Research (NIMR), New Delhi | Ministry of Health and Family Welfare (MoHFW) | Research Institutions | Delhi |
| National Institute of Medical Statistics (NIMS) | Ministry of Health and Family Welfare (MoHFW) | Research Institutions | Delhi |
| National Institute of Mental Health & Neuro Sciences (NIMHANS) | Ministry of Agriculture and Farmers Welfare (MoAFW) | — | Karnataka |
| National Institute of Natural Fibre Engineering and Technology (NINFET) | Ministry of Agriculture and Farmers Welfare (MoAFW) | — | West Bengal |
| National Institute of Nutrition (NIN), Hyderabad | Ministry of Health and Family Welfare (MoHFW) | Research Institutions | Telangana |
| National Institute of Occupational Health (NIOH), Ahmedabad | Ministry of Health and Family Welfare (MoHFW) | Research Institutions | Gujarat |
| National Institute of Oceanography (NIO) | Ministry of Science & Technology (MoST) | — | Goa |
| National Institute of Ocean Technology (NIOT) | Ministry of Earth Sciences (MoES) | Research Institutions | Tamil Nadu |
| National Institute of Open Schooling (NIOS) | — | Research Institutions | Uttar Pradesh |
| National Institute of Pathology (NIP), New Delhi | Ministry of Health and Family Welfare (MoHFW) | Research Institutions | Delhi |
| National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad | — | — | — |
| National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad | Ministry of Chemicals and Fertilizers (MoCF) | — | Telangana |
| National Institute of Pharmaceutical Education and Research (NIPER), Kolkata | — | — | — |