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Security Sector Reform in Indonesia commenced since there had been strong demand for TNI to abandoned its Dwi Function Role, followed by the prescribed MPR Decree No VI/2000 on the Separation of TNI and POLRI and MPR Decree No VII/ 2000 on the Role of TNI and POLRI. The separation of TNI-POLRI envisaged a good political decision in order to attain professional TNI and POLRI. However, that political response is not followed by the arrangement of a comprehensive National Security system, in which national security instruments are not yet integrated, still partial, and has dichotomy between defence and security without inter-linkage among them. It can be seen since the TNI-POLRI Separation, a number of problems escalate when the laws cannot anticipate the grey area that result to confusions in the authority level and in the end triggering hesitation, misunderstanding, rivalry, and even dispute between security apparatus in the field. The absence of clear regulation which affirms the TNI-POLRI Relations hampers the efforts to manage national security issues.Post Separation, Indonesia experienced endless complicated issues of internal security such as separatist act in Aceh, Papua and Maluku, communal conflict in Maluku and Kalimantan and terrorist act in some regions. Besides that, vigilante violence by groups of community flourish in our country. Somehow, the outbreak of violence might be inevitable if security apparatus do not have the readiness and the capability to anticipate regarded that threat which is faced today is azimuthal. Although, the handling of internal security sector is exclusively police responsibility, including upholding the law and order, the current police capacity is considered weak. Therefore, the capacity of POLRI needs to be strengthened before confining TNI only for external defence. POLRI still lacks of operational capability in numbers and trainings, while TNI faces the dilemma between actual demand and authority. So, the consideration is needed on how to define a transitional role for the military in handling internal security while police capacity is being developed, without further blurring the lines between them. In the other side, the problems get more complicated worrying make anxiety when the intensity of physical clash between TNI-POLRI persons is happening frequently. This clash has resulted loss of lives, material damage and unnecessary casualties from the civilians. The phenomena that were mentioned above exemplify that TNI-POLRI Relations run into such constraints which lead to ineffectiveness.The objectives of this thesis are to identify factors constraining to TNI-POLRI Relations, then to find out the efforts for developing TNI-POLRI Relations within the good governance framework that reliable to cover internal security issues and may contribute to overcome the clash between TNI-POLRI persons. The research methodology uses the qualitative-descriptive-deductive methods with approach by a case study of TNI-POLRI task force in handling internal security issues in Maluku. The sources of data are primary data by using the techniques of interview and observation, and also secondary data by literature studies.The result of research outlines that the emerge of constraint starts from the over-simplification on national security, the laws are not consistent and overlap causing TNI-POLRI Relations ineffective. Meanwhile, at operational level, ineffective performance of security apparatus in handling the wider threat to security in Maluku was caused by the lacks of cooperation, communication and cooperation between TNI-POLRI. It led to transitional management for internal security did not go smoothly from TNI to POLRI and vice-verse in which there was dispute on the hand of authority. Both TNI and POLRI did not give concern on the grey area that should be fulfilled through cooperation, communication, and coordination. It is because the absence of Laws which clearly regulate the engagements.