This study raises the problem of disharmonization of norms in the recognition and protection of customary rights of customary law communities, due to constitutional recognition through Article 18B paragraph (2) of the 1945 Constitution which is conditional as Article 3 of the UUPA, while the subsequent arrangements are scattered fragmentarily in unintegrated sectoral regulations. This condition triggers repeated agrarian conflicts, recorded in 217 cases throughout 2024 with an affected area of 630 hectares. This study aims to analyze the legal construction of the recognition and protection of customary rights in the national legal system and formulate an ideal legal reconstruction. The method used is a prescriptive normative legal research, with a legislative, conceptual, case, and comparative approach to the Philippines and Ethiopia. Primary, secondary, and tertiary legal materials were collected through literature studies, then analyzed qualitatively-normatively using grammatical, systematic, telelogical, and deductive logic interpretations. The results of the study show that the existing legal construction is still fragmentary, because conditional recognition in the UUPA is not followed by the harmonization of sectoral regulations, so customary rights are often subordinate to investment interests, even though the Constitutional Court Decision Number 35/PUU-X/2012 has corrected some of the inequality through the restoration of customary forest status. This research develops a legal construction that operationalizes the paradigm shift from conditional recognition to existence and history-based recognition, through the expansion of tiered recognition mechanisms, the determination of customary territories, preventive-repressive protection, regulatory harmonization, cross-agency institutional models, and tiered dispute resolution. These findings affirm the declarative nature of state recognition of customary rights and offer a framework for improving the Customary Law Communities Bill. Further research is recommended to test this reconstruction empirically in various regions.