Studies on innovation point towards the need for both in-house research and development (R&D) capabilities along with collaborations with external organisations or linkages with other firms, universities and research institutes. The argument is that innovation is not just a firm specific factor but requires support from several other factors which in turn involves developing linkages with various actors/institutions as sources of resources and/or knowledge for innovation. This paper presents findings from an exploratory study about the Malaysian biofuel sector as an innovation system. Instead of using the neo-classical approach and proposing policy interventions based on traditional market failure rationale (Bergek et al., 2008a), the functional analysis of the technological innovation systems (TIS) approach is used to analyse the biofuel sector in Malaysia to help reveal the strengths and weaknesses in terms of its fulfillment of seven critical functions which are necessary for the generation and commercialization of a product. In addition an attempt is made to reveal the inducement and blocking mechanisms affecting the Malaysian biofuel TIS and the seeking of improved poor functionality. These functional aspects of the Malaysian biofuel sector are analysed in different phases of its development to gain an understanding of the different institutions and their functions at different phases of the development of the innovation system.