At the central level, the Ministry of interior is responsible for all matters in relation to refugees. Article 54 of the law n.1/32 of 13 November 2008 on asylum and the protection of refugees in Burundi provides that admission to refugee status is subject to an order by the Minister of Interior. Article 62 of the same law also provides that the loss of refugee status is subject to an order by the Minister of Interior.

At the sub central level, there are three entities:

• The Consultative Commission for Foreigners and Refugees (CCER): Article 2 of Ordinance No.530/443 of 07/04/2009 on implementing measures for Law No 1/32 of 13 November 2008 on asylum and refugee protection in Burundi and on the composition, organization, and operation of the CCER and the Appeals Committee provides for the missions of the CCER and states that the CCER:
• Ensures the physical, material, legal and administrative protection of asylum seekers and 
•  examines and decides on applications for refugee status and any influx of refugees or asylum seekers, in accordance with current international standards and practices.
• Examines and decides on applications for derived refugee status.
• Decides on the termination of refugee status by cessation, annulment or revocation.
• Gives its opinion prior to the execution of any expulsion or refoulement order.
• Examines requests for resettlement in Burundi and, in the event of a favourable decision, to take all necessary steps to facilitate the reception of refugees in the best possible conditions of safety and dignity.
• Studies and proposes to the Government any measure likely to improve the living conditions of refugees and asylum seekers in Burundi and to seek lasting solutions to refugee problems.
• Provides, within the means at its disposal, for the needs of refugees and asylum seekers on Burundian territory under the protection of the Government in matters of, inter alia, food, housing, health and education, it being understood that it may, for this purpose, call upon the assistance of national and international organizations concerned with the problems of refugees and asylum seekers.
• The Appeals Committee / Comité de recours (CR): According to articles 23 and 24 of Ordinance no. 530/443 of 07/04/2009 on implementing measures for Law no. 1/32 of 13 November 2008 on asylum and refugee protection in Burundi and on the composition, organization, and functioning of the CCER and the Appeals Committee, the CR receives and examines appeals lodged by asylum seekers against negative decisions of the CCER. The CR is the last instance. It also hears, in the last instance, decisions made by the CCER concerning any matter relating to refugees and asylum seekers, particularly in relation to expulsion and deportation.
• The National Office for the Protection of Refugees and Stateless Persons (ONPRA): according to article 2 of decree n. 100/069 of 30 May 2022 on the organization, missions, and functioning of the National Office for the Protection of Refugees and Stateless Persons, ONPRA is a technical structure responsible for the management of asylum and the protection of refugees and stateless persons. It is placed under the supervision of the Minister responsible for refugee management. 

At the local level, there are registration centers, the management of which is entrusted to the consultative commission may be created by the Minister having the interior in his attributions. Registration centers are a starting point for all refugees. The functions of the registration centres makes them closer and more accessible to refugees than the other administrative entities are.

According to article 78 of the law n.1/25 of 05 November 2021 regulating migration in Burundi, registration and transit centres may be created in the event of a mass influx of asylum seekers, in which case they are jointly created by the ministers responsible for territorial administration and public security. They are managed by ONPRA and secured by the police. A registration or transit centre may not be set up in the neutral zone and no other activity may be carried out there.

As of their functions, article 50 of the law n.1/32 of 13 November 2008 on asylum and the protection of refugees in Burundi states that the registration center collects the applicant's personal data, fingerprints, and photographs. It may summarily question the applicant about the reasons why he or she left his or her country and the route he or she took. 

Also, asylum applications may be deposited at a registration center according to article 75 of the law n.1/25 of 05 November 2021 regulating migration in Burundi. 

In cases where an asylum application is submitted at the border, article 31 of law n.1/32 of 13 November 2008 on asylum and the protection of refugees in Burundi provides that the border post or registration centre shall authorise the entry into Burundi of the person wishing to apply for asylum.