The article analyses Japanese approaches to dealing with eco-efficiency from aninstitutional perspective. Our main outlook is that though promising attempts havebeen made despite the overall economic crisis, a better horizontal coordinationamong both administrations and businesses is required. The governance processescan be analysed following approaches developed by New Institutional Economicsand related policy analysis. The paper is divided into three sections. The first introduces the concept of eco-efficiency and explains the demand for regulatorypolicies from theories of market failures; the paper argues in favour of innovation-oriented regulation. The second examines how a nation's institutional capabilitiesinfluence knowledge generation towards new solutions that sell on the markets;the capacity-building approach as developed by Martin Jänicke is explicitly discussed. The third section discusses contemporary Japanese policies with regardto waste, energy and material flows both on the governmental and the businesslevel. It explains how European approaches diffuse and merge with domestic Japanese institutions. However, governance of eco-efficiency is expected tocontinue to differ due to ongoing national differences and specific conditions of knowledge creation.