This paper concerns accountability and agency concepts in governance reforms in Indonesia. The country's economic crisis in 1997, which snowballed into social and political crisis, triggered the country to reform the governance of the ministries by transferring government functions from ministries to agency-type organizations. However, this reform has led to rising questions about the accountability arrangements of the newly formed organisations which are oriented to agency-based governance. In addition, there are several different arrangements for these agencies. This study aims to analyse the extent to which accountability is accorded in various types of agencies. In doing so, the study uses typology of the government agencies as a tool to understand the accountability through its autonomies. The results indicate that the variety of agencies' forms requires a different accountability setting, which is not being met in the current regulations.