Besides making pioneering contribution in the domain of Soil Science, Dr Mukherjee played a key role in the development of agricultural research and education in the country. Soon after his appointment as Director of the Imperial (now Indian Agricultural Research Institute, New Delhi), in 1945, Dr Mukherjee began to 
reorganise the research and educational activities of the Institute in the country as a whole. Under his direction the Institute expanded considerably in terms 
of its academic activities and scientific performance. He initiated research in the area of soil-plant studies. Some of the sections he created in the Division of Soil Science and Agricultural Chemistry are Soil Survey, Soil Physics, Agricultural Chemistry, Soil Fertility, Soil Microbiology, Biochemistry, Organic Chemistry and Spectroscopy. Recent expansion of some of the sections such as Soil Survey, Microbiology, Biochemistry, Agricultural Chemicals, Agricultural Physics were credited to him. 
The credit for initiating systematic studies on micronutrient elements in soils and plants and also on clay mineralogy of soils with the help of sophisticated instruments and modern techniques goes to him. He initiated work in the Institute on the nutritive value of foods, feeds and fodders, on insecticides and fungicides, and on the chemistry of plant products.
He was the first in the country to lay great emphasis on the importance of soil surveys for agricultural development and underlined the importance of uniformity in the methods of survey, classification and nomenclature of the soils of India. At his suggestion the Ministry of Agriculture, Government of India established in 1949 the Central Committee on Soil Science with him as chairman. The terms and reference of the Committee were practically in conformity with the objectives of the All India Soil and Land Use Survey Organization established in 1956 with 4 regional centres. 
The soil map of India revised under his guidance (scale 1" --- 70 miles) showing 20 soil classes was published in 1954. He also developed the concept of the 
basic soil regions in the classifications of the soils of India based on similar characteristics of land viz.., the climate, topography, vegetation and soils.