The application of information and communication technology (ICT) is a phenomenon that permeates many aspects of government practices since the end of the last century. E-government has been growing rapidly following the development of E-commerce. More than the application of ICT, international aid agencies expect that E-government can be a tool for the governance transformation efforts in developing countries. Government of Indonesia's initiative to develop E-government has been strengthened in various government policies since 2001. The Indonesian government has set up many programs to keep pace in the field of E-government. Basically, the government is aware of the constraints of priority in public finance, lack of technology and human resources. Therefore, since 2001 the government has initiated the development of E-government through public-private partnerships. However, apart from the aspects of ICT and capital, as well as the availability of human resources, the implementation of public-private partnerships in the development of E-government has not been held smoothly. Developing E-government through public-private partnerships could potentially be facing institutional barriers. Therefore, the implementation of E-government in Indonesia, which is expected to be done by a public-private partnership schemes are susceptible to situations of uneasy. Inequality in institutional arrangements has been slowing the progress of the program. So, the two parties have not yet able to achieve greater benefits from the partnership.