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The National Clean Energy Fund (NCEF), announced in Budget 2010-11, is seen as a major step in India's quest for energy security and reducing carbon intensity of energy. Funding research and innovative projects in clean energy technologies, and harnessing renewable energy sources to reduce dependence on fossil fuels constitute the objectives of the NCEF. It is observed that utilization of funds from NCEF has been rather low and disbursements, so far, are aligned more with on-going programmes/missions of various ministries/departments than with the stated objectives of the Fund. This poses potential risk of diluting the focus of NCEF with adverse implications for research and innovation in the clean energy sector in India, especially, in the absence of any identified targets and prioritization. This study has provided a detailed framework for promoting effective utilization and administration of NCEF.