In the effort to address flood problems in Jakarta, the Indonesian and Dutch Government finalized a study called Jakarta Coastal Defence Strategy (JCDS) in 2011. In the study, it is concluded that an offshore solution is crucial to protect Jakarta from the threat of sea level rise in the coastal area. The collaboration between these two countries was later continued by realizing the Master Plan for the National Capital Integrated Coastal Development (NCICD). The main purpose of this master plan is to provide a long-term solution for flooding problems. In addition to the main purpose, this plan also addresses other urban problems, proposes a solution to improve the coastal zone area and facilitates socio-economic development in the area. This project encounters high resistance from public and is deemed to be controversial in the public domain as the plan includes the construction of a large protection wall enclosing the sea and land reclamation. The public perceives that this project would have fatal environmental and social impacts, including the disappearance of mangrove forest, undesirable effect on the livelihoods of vulnerable communities, etc. Hitherto the plan has remained controversial, despite formal assessment conducted by the Indonesian government and Dutch consultants, in which the plan is considered as a measure to save Jakarta from being a sinking city caused by an alarming rate of land subsidence. Noting this constant debate of the project, identifying values of stakeholders is, therefore, important to understand the underlying reasons of persistent oppositions. Hence the objective of this research is to develop an approach for mitigating conflicting values in a public project in Indonesia as the supporting tool for decision making process. To be able to understand the decision-making process and identify the values at stake, an analysis was performed based on 243 newspaper articles which were selected using the keywords: ‘giant sea wall’ and ‘NCICD’ within a time period of 57 months; from January 2011 to September 2016. From these articles, the decision-making process was constructed to analyze how the decision-making process was conducted in the past and what important aspects have been missed in the implementation of decision-making process. In addition, values of the stakeholders were also identified by analyzing the arguments set forth by diverse stakeholders. From the previous literature and analysis in this research, it has been observed that there are certain stakeholders who are necessary to be involved but are still underrepresented in the plan. Furthermore, the values which are fundamental to certain stakeholders have not been covered in the previous assessments. Therefore, in this research, the values of stakeholders are adopted as the basis of using expert methods in decision-making process in combination with the stakeholder participation method. To conclude this research, the following list is the summary of the developed approaches in which an adapted version of existing methods are used to address specific value conflict: EIA and MCA as the method to mitigate the value conflict of safety, economic development vs environmental protection (i), CBA as a method to mitigate safety, economic development, cost-recovery vs economic and welfare (general), utilities (ii), VSD as the method to mitigate value conflict between safety, economic development vs economic and welfare (affected communities), culture/ Identity (iii), and VSD as a method to mitigate value conflicts between safety, economic development vs port development (economic interest) (iv).