This paper addresses the nature of Chilean investment in science, research and innovation and how this feeds into a broader narrative of productivist versus regional development, with a particular focus on natural resources. The concept of neostructuralism is employed to describe this productivist public sector support for investment in science and policy in relation to socio-economic and environmental research. Against this productivist perspective, a responsible research and innovation (RRI) approach is highlighted which is characterized by contextual, geographical relevance rather than generic solutions: sustainable regional development. Examples are drawn from mining and aquaculture to provide sectoral detail of this productivist logic: the case of mining reveals the focus on generating a cluster while the dimensions of indigenous conflicts and water stress are left to critical social sciences, while aquaculture provides examples of state support for aquaculture promotion with comparatively little investment in impact studies and conflicts. The conclusions point to a strong bias in science and development policy towards product innovation and the protagonism of the private sector allied with science policy support, while sustainable regional development and the role of the decentralized public sector is relegated to a more marginal field of ‘critical’ research.