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- ICAR Awards for Team Research for the Biennium 1999-2000 for outstanding research contribution in the field of animal disease management.
- Lal Bahadur Shastri Young Scientist Award for Agricultural Research for the Biennium 1999-2000.
- Sardar Patel Outstanding ICAR Institution Award 2001 for outstanding contribution in the field of animal disease monitoring and surveillance.
- DBT Biotech Product Process Development and Commercialization Award 2002 for its outstanding contribution for the development of software based veterinary ELISA diagnostic kits for the detection of the infections Bovine Rhinotracheitis (IBR) and Bovine Brucellosis in serum and milk as well as recombinant competitive ELISA kit for Rinderpest.
- OIE Meritorious Award by OIE, Paris in 2002.
- FAO gold medal for outstanding contribution to global rinderpest eradication programme, 2011.
- ISO 9001:2008 certificate awarded to NIVEDI on 2014.