The Department of Internal Boundaries is headed by a Director and works in conjunction with States and Local Government Boundary Committees and it liaises with other relevant Federal Government Agencies. The Department is responsible for handling disputed Boundary cases where they exist and/or when reported. It also initiates intervention process to take advantage of existing peace to define Boundaries. The Department functions as follows:
The National Boundary Commission Establishment Act, 2006 provides the following for the Commission with regards to Internal Boundaries:

i. Intervene, determine and deal with any Boundary dispute that may arise among States, Local Government Areas or Communities in the Federation with a view to settling the dispute,
ii. Define and Delimitate Boundaries between States, Local Government Areas or Communities in the Federation in accordance with Delimitation Instrument or Document established for that purpose,
iii. Facilitate Equitable Utilization of Shared Border Resources of Land, Water, Games, Forest Resources, etc.,
Formulate Policies and programmes on Internal Boundaries,
iv. Take all necessary steps towards the Implementation of Resolutions on Internal Boundary Disputes, and
v. Disseminate Information to Educate the General Public on Functions of the Commission.
The above functions are executed by the Commission through its Inter-State Boundary Technical Committee (IBTC) and the Internal Boundaries Department. Accordingly, the department’s activities further include:
i. Correspondences with States, Local Government Areas and affected Communities on reported Boundary Disputes,
ii. Search for relevant documents on Boundary cases through the Zonal Liaison Offices,
iii. Independent Investigations on reported disputed cases through the Zonal Liaison Offices,
iv. Requests for additional inputs from State Boundary Committees on reported cases,
v. Convening of Joint Meeting of Officials in the States concerned to initiate discussion with Stakeholders,
vi. Fieldwork on the Boundary (Tracing and Provisional Demarcation, Boundary Testing or Ground-to-Pater Data Gathering),
vi. Articulation of Findings and Recommendations for the attention and consideration of the Internal Boundary Technical Committee,
vii. Convening meetings of the Internal Boundary Technical Committee,
viii. Acting on appropriate directives of the IBTC (may include additional fieldwork, etc.),
ix. Advocacy visits to disputed Border Communities (Sensitization and Enlightenment Campaigns on Essence and Imperatives of Peaceful Co-existence),
x. Participation and Monitoring in Boundary Tracing and Provisional Demarcation, and
xi. Organizing Workshops and Seminars to Sensitize and Enlighten the Public on issues of Boundary as well as Dispute Resolution and Management.