Honduras' international protection framework involves several institutions at the national and local levels. However, refugee status determination (RSD) remains centralized within the National Institute of Migration (INM), which is responsible for processing asylum applications and coordinating the administrative procedures leading to a decision. The Secretariat of State for Governance, Justice, and Decentralization exercises political and regulatory functions related to migration and international protection. The National Institute of Migration (INM) is responsible for the operational implementation of the asylum system, including the processing of refugee status applications and the issuance of Special Residence Permits pursuant to Article 8 of the Migration and Aliens Law (Decree No. 208-2003). In accordance with Article 51 of the same Law, refugees wishing to travel abroad may apply to the INM for the issuance of a travel document. Furthermore, Article 69 authorizes the issuance of passports and emergency travel documents to recognized refugees, asylees, stateless persons, and foreign nationals whose countries of origin do not have accredited diplomatic or consular representation in Honduras. At the sub-national level, the INM operates through a network of migration delegations, including border, airport, land transit and internal control offices, as well as Centers for Assistance to Irregular Migrants (CAMIs), which support migration management and facilitate access to protection procedures throughout the national territory. Pursuant to Article 107 of the Migration and Aliens Law, all civil and military authorities are required to cooperate with migration officials, upon request, in the implementation of the Law, its Regulations, and administrative measures adopted under Honduras' migration policy framework. Internally, the INM's Human Rights and Migrant Assistance Directorate conducts initial screenings and eligibility interviews, while the Commission of Refugee collectively evaluates case files and issues the advisory opinion underpinning the final resolution. UNHCR provides technical, operational, and financial support to the asylum system, including institutional capacity development, procedural strengthening, and support for protection responses, in line with its global mandate and strategic priorities, including through the Comprehensive Regional Protection and Solutions Framework (MIRPS).

The system faces three structural gaps:

Financing: There are no dedicated budgetary allocations for international protection. Operations depend largely on the INM's ordinary budget and support from international cooperation partners. The INM's budget is subject to annual approval by the National Congress.

Inclusion Gaps: Asylum-seekers are documented through temporary stay authorizations while their claims are being processed, whereas recognized refugees are granted a Special Residence Permit (Permiso Especial de Permanencia - PEP), generally issued for a five-year period. While these documents provide lawful stay and access to international protection, they do not confer permanent residence status. Their legal classification and varying levels of recognition by some public and private institutions may create administrative barriers to accessing formal employment, financial services, social security mechanisms, and broader socioeconomic inclusion.

Monitoring: Honduras does not have a specialized institution exclusively mandated to monitor the rights of asylum-seekers and refugees. However, the National Commissioner for Human Rights (CONADEH), as the country's national human rights institution, plays an important role in monitoring the protection of human rights, receiving complaints, and promoting access to rights for vulnerable populations, including asylum-seekers, refugees, internally displaced persons, and other persons in situations of human mobility. Additional monitoring and protection functions are carried out by UNHCR, civil society organizations, and other actors supporting the international protection system. While these mechanisms contribute to oversight and accountability, there is no dedicated institution solely responsible for monitoring compliance with refugee rights and international protection standards.

For internally displaced persons, the Secretariat of Human Rights (Secretaría de Derechos Humanos, SEDH), through its Directorate for the Protection of Persons Internally Displaced by Violence (DIPPDIV), leads prevention, protection and assistance efforts. Its response includes temporary accommodation, relocation, legal guidance, psychosocial support, material assistance and livelihoods support. The Law for the Prevention, Assistance and Protection of Internally Displaced Persons establishes the National Response System to Internal Forced Displacement (SINARDEFI) as the framework for a coordinated State response. 

The Inter-Institutional Commission for the Protection of Forcibly Displaced Persons (CIPPDEF) provides inter-institutional coordination for implementing the internal displacement framework. Its work includes developing policies and protocols, coordinating prevention and assistance measures, promoting resource mobilization and monitoring implementation. Civil society participates in the Commission.

The Municipal Units for the Assistance and Protection of Forcibly Displaced Persons (UMAPPDEF) are the local implementation mechanism envisaged under Honduras’s Law for the Prevention, Assistance and Protection of Internally Displaced Persons, they form part of the national response system, alongside the Inter-Institutional Commission for the Protection of Forcibly Displaced Persons (CIPPDEF) and the Directorate for the Protection of Persons Internally Displaced by Violence (DIPPDIV). The framework envisages their operation in municipalities with the highest numbers of displaced persons or persons at risk of displacement.