The period following the overthrow of the Marcos regime brought important changes to the Philippines' intelligence and security structure. During the martial law era (1972-81), the volume and scope of government intelligence activity had greatly expanded. The preeminent intelligence agency was the National Intelligence and Security Authority, headed by General Fabian Ver, a close Marcos confidant and chief of staff of the Philippine armed forces. By the end of Marcos's tenure, the National Intelligence and Security Authority and the rest of the country's intelligence apparatus were heavily focused on tracking the president's political opponents. Security agents were suspected of numerous human rights abuses.

The revamp of the nation's intelligence system commenced with Aquino's rise to power. The new government significantly curtailed intelligence operations and purged many of General Ver's operatives. Drafters of the 1987 constitution installed legal safeguards against the kind of abuses committed by the Marcos intelligence and security apparatus. The National Intelligence and Security Authority, tainted by its close association with the deposed president, was renamed the National Intelligence Coordinating Agency and refocused its efforts away from political opposition leaders to internal security threats, especially the communist insurgency. Notable intelligence successes against the communist rebels during the late 1980s were an apparent result of this reorientation. Government operatives repeatedly captured top CPP and NPA cadres, prompting devastating purges within the insurgent ranks as guerrillas attempted to ferret out the sources of intelligence penetrations.

In 1990 Aquino issued an executive order authorizing her national security adviser to oversee the National Intelligence Coordinating Agency and other elements of the intelligence community. The adviser was empowered to audit the agencies and was charged with ensuring that they were responsive to the needs of the president and the National Security Council. The secretaries of national defense and justice, whose departments performed intelligence functions, were directed to work with the national security adviser to fulfill the president's mandate.

The Department of Justice's principal intelligence-gathering organ, the National Bureau of Investigation, was formed in 1936 as the Division of Investigation and patterned after the United States Federal Bureau of Investigation. The bureau's principal mission was to assist the Philippine Constabulary and police in crime detection and investigation, freeing them to concentrate on maintaining peace and order. Collection of intelligence on internal security threats was considered a related function.

The Department of National Defense, meanwhile, maintained an extensive intelligence apparatus. Although little was publicly revealed about its organization or operation, it was known that the military's principal intelligence organ was the Intelligence Service of the AFP. Headed by a brigadier general, Intelligence Service units operated througho358 hout the country. Their mission in 1990 included not only pursuing insurgents, but also gathering information on military coup plotters and participants. The military services, too, maintained their own intelligence arms. The regimental-size Intelligence and Security Group supported the army while the Constabulary Security Group served Philippine Constabulary leaders. The division of responsibilities among these military intelligence agencies, as well as the institutional mechanisms, if any, that were set up to coordinate their activities, were unclear.

Data as of June 1991