This study aims at examining and analysing factors that cause weaknesses in internal control system of provincial local government. Population of this study is all 34 provincial governments in Indonesia and the studied object is internal control weaknesses identified in the Provincial Government Audit Reports produced by the Audit Board of the Republic of Indonesia. Eighty three reports were used as sample ranging from 2011 to 2015. The research model of this study indicates adjusted R2 at 86% which is much higher than previous studies on this topic, Based on the multiple regression analysis, it is found that the size of local government and the use of information technology have a significant negative effect on the weaknesses of internal control. This implies that Provincial Government needs to use more information technology and allocate more resources on internal control improvement. On the other hand, the complexity of local government and the quality of human resources have positive effect on the weaknesses of internal control. These findings suggest provincial governments with large number of sub-districts to put more efforts in internal control system improvement than others. The provincial government with higher human development index needs more efforts on ethical conduct. This study contributes in investigating both financial and non-financial factors affecting internal control weaknesses of provincial government for longer period of analysis.