Under Executive Order 246, the NICA is mandated to be the focal point for the direction, coordination and integration of government activities involving national intelligence, and the preparation of intelligence estimates of local and foreign situations for the formulation of national policies by the President.

Under Executive Order 69, the NICA shall institute structural reforms to enable the Agency to sufficiently respond to the challenges of the new millennium, enhance its intelligence assessment and operational competence, strengthen its capability for intelligence collection, and allow it to take the lead in intelligence management.

Administrative Order (AO) 68, among others, further designated the DG, NICA as the principal adviser to the President on intelligence. Under AO 68, the DG, NICA chairs the National Intelligence Committee (NIC), a collegial body tasked to promote unity and cohesion of the national intelligence community as well as prescribe policy guidelines and directives to various national government units, agencies and offices engaged in activities involving national intelligence.

The NICA also acts as coordinator for government security under EO 608, which calls for the establishment of a national security clearance system for government personnel. 

             Section 53 of Republic Act (RA) 9372 or the Human Security Act of 2007 provides that the NICA shall be the Secretariat of the Anti-Terrorism Council. The Council shall define the powers, duties and functions of the NICA as Secretariat of the Council.