The evolution of information, communication and technology (ICT) brings many benefits in the relationship between citizens and governments to offer better services in public sector. But, in the fact e-participation implementation faces many challenges and issues especially in developing countries. Digital divide, lack skilled people and poor citizen education becomes a factor that impede e-participation implementation. This study aims to explore and analysis challenge and issues of e-complaint implementation in Indonesia. The interview was conducted using semi-structured in two weeks with the expert and citizen. The selection of the expert and citizen as participant was conducted using purposive sampling. STOPE framework used over this study to analyze and to keep objective of the research in context. There are 10 sub-domains based on STOPE framework analysis as the challenges and issues of e-complaint in Indonesia. Those are political bureaucracy commitment, promoting strategy, security privacy, lack skilled people in organization, team coordination, lack of training in organization, poor citizen education, trust, digital divide and social culture. Challenges and issues of e-complaint in Indonesia can analyze to provide insight that can be used for developing better e-complaint platform in Indonesia. © 2018 IEEE.