Chilakampally Narayana Reddy Gold Medal for securing highest OGPA in M.V.Sc. (Microbiology) from College of Veterinary Science, Tirupati at the 29th Annual Convocation, Andhra Pradesh Agricultural University (9th Jan, 1998)

Awarded Dr S Vancheeswara Iyer Memorial Gold Medal by the Indian Veterinary Association in 2001 for the best paper ‘An indirect IgM-ELISA for diagnosis of sheep pox virus infection - B. Madhusudana Rao and M. V. Subba Rao’ published in Indian Veterinary Journal, 76 (12): 1050-1054; 1999 

Best paper award given by the Society of Fisheries Technologists (India), Cochin in 2004 for the paper ‘Microbial Populations in Deep Sea Water and Fish of South East Arabian Sea with special emphasis on Escherichia coli and Coliphage- B. Madhusudana Rao and P. K. Surendran.’ published in Fishery Technology, 40 (2): 105 – 114; 2003.

Network of Indian Agri-Business Incubators (NIABI) National Award for Best Agri-Business Incubator for the year 2013 was awarded to the Zonal Technology Management & Business Planning and Development (ZTM-BPD) Unit, Central Institute of Fisheries Technology (CIFT), Cochin during the Indian Agri-Business Incubation Conference, 26 April 2013, Hyderabad.

Best paper Award for the paper titled ‘Nutritional and physical properties of noodles incorporated with Seaweed puree- Jesmi Debbarma, Viji P., B.Madhusudana Rao, and M.M. Prasad” presented at by Jesmi Debbarma at “National Seminar on Fisheries and Aquaculture: Lively hood security, sustainability and conservation"" in the Technical session: Harvest and Post Harvest Technology, held on 21-22 January, 2016 at College of Fisheries, Lembucherra, Tripura.