Agrarian conflict in Papua reflects a persistent tension between the state-centered orientation of Indonesia’s national land law and the communal land tenure system of Papuan indigenous communities. The expansion of investment activities, the implementation of national strategic projects, and the limited formal recognition of customary land rights have reinforced asymmetrical legal pluralism and intensified agrarian disputes. This study examines the structure of legal pluralism in Papuan agrarian conflicts, analyzes customary-based dispute resolution mechanisms, and formulates a reconstruction model for indigenous-based land governance. The study employs a normative-empirical socio-legal design combining statutory, conceptual, case, and comparative approaches. The study collected empirical data through semi-structured interviews with customary leaders, government officials, academics, and indigenous community members in Manokwari and Biak Numfor, supported by field observations and document analysis. Data were collected through a literature review, regulatory analysis, judicial decisions, and empirical studies concerning agrarian conflicts in Papua. The findings demonstrate that customary dispute resolution mechanisms possess strong social legitimacy but remain structurally marginalized within the formal state legal system. The study contributes to legal pluralism scholarship by developing the concept of coordinated legal pluralism, an operational governance model designed to integrate customary law and state law within Papua’s agrarian governance framework. The study concludes that agrarian governance in Papua requires institutional integration between customary and state legal systems. It recommends formally recognizing customary mediation outcomes, reforming evidentiary rules, implementing FPIC requirements, and strengthening indigenous governance institutions to reduce agrarian conflicts and improve legal certainty.