This study empirically examines the impact of audit opinions, internal control system weaknesses, bureaucracy reform and the political background of ministries and government institution leaders on the level of corruption in Indonesia. This study, involving a sample of 86 ministries in 2011 and 2012, was processed by categorical and non-parametric statistical methods, and revealed that weaknesses of the internal control system and the political background of the leaders were factors that may affect the probability of corruption, while audit opinions and bureaucracy reform were proved to have no significant impact on the probability of corruption. Therefore, the Indonesian government must increase its control in those ministries that have leaders with a political background and must also make improvements to the internal control system of government agencies.