Click on the names to visit respective website.
| Rank | Name | Established In | Course Offered |
|---|
| 1. | Homi Bhabha National Institute (HBNI), Mumbai | 2005 | PhD |
| 2. | Indira Gandhi Centre for Atomic Research (IGCAR), Kalpakkam, Tamil Nadu | 1971 | PhD |
| 3. | Raja Ramanna Centre for Advanced Technology (RRCAT), Indore | 1984 | PhD |
| 4. | Variable Energy Cyclotron Centre (VECC), Kolkata | 1977 | PhD |
| 5. | India-based Neutrino Observatory (INO) | | PhD |
| 6. | Bhabha Atomic Research Centre (BARC), Mumbai | 1954 | PhD |
| 7. | Tata Institute of Fundamental Research (TIFR), Mumbai (Deemed University) | 1945 | PhD |
| 8. | Tata Institute of Fundamental Research (TIFR), Hyderabad (Deemed University) | 1945 | PhD |
| 9. | International Centre for Theoretical Sciences (ICTS), Banaglore (Centre of TIFR) | 2007 | PhD |
| 10. | National Institute of Science Education and Research (NISER), Bhubaneswar | 2006 | PhD |
| 11. | National Board for Higher Mathematics (NBHM), New Delhi | 1983 | PhD |
| 12. | Centre for Excellence in Basic Sciences | 2007 | PhD |
| 13. | Saha Institute of Nuclear Physics (SINP), Kolkata | 1949 | PhD |
| 14. | Institute of Physics (IOP), Bhubaneswar | 1972 | PhD |
| 15. | Harish-Chandra Research Institute (HRI), Allahabad | 1975 | PhD |
| 16. | Institute of Mathematical Sciences (IMSc), Chennai | 1962 | PhD |
| 17. | Institute for Plasma Research, Gandhinagar | 1986 | PhD |
| 18. | National Centre for Radio Astrophysics (NCRA), Pune University Campus (Part of TIFR) | 1960 | PhD |
