Bhatnagar played a significant part along with Homi Jehangir Bhabha, Prasanta Chandra Mahalanobis, Vikram Sarabhai and others in building of India's post-independence science and Technology infrastructure and policies. Prime Minister Nehru was a proponent of scientific development, and after India's independence in 1947, the Council of Scientific and Industrial Research (CSIR) was set up under the chairmanship of Dr. Bhatnagar. He became its first Director-General, and by his works he is largely remembered for having established various chemical laboratories in India. He established a total twelve national laboratories such as Central Food Processing Technological Institute, Mysore, National Chemical Laboratory, Pune, the National Physical Laboratory, New Delhi, the National Metallurgical Laboratory, Jamshedpur, the Central Fuel Institute, Dhanbad, just to name a few. While at CSIR, he mentored a number of promising young Scientists of the time who were working in the very productive climate in those days at the Indian Association for the Cultivation of Science (IACS) in Kolkata, including Syamadas Chatterjee, Santilal Banerjee (MSc Gold Medalist- Dacca University and a DSc from the US) who later moved to the National Physical Laboratory in Delhi at Bhatnagar's urging), Asutosh Mookherjee etc. Bhatnagar also closely followed the work of C. V. Raman and Kariamanickam Srinivasa Krishnan at IACS on the Raman Effect and in particular the work Krishnan and his partner, Santilal Banerjee, were doing on the magnetism of small crystals.