Starting in 1987 a new, unsettling element clouded civilmilitary relations: vigilante groups that hunted down suspected communists and other leftists. The first and most famous such group was Alsa Masa (Masses Arise), which virtually eliminated communist influence from the Agdao slum area of Davao City. The potential for civilians to accomplish what the military could not aroused official interest. Soon there were more than 200 such groups across the country, with names that hinted at their violent, cult-like nature: Remnants of God Guerrero of Jesus Sin, Salvation, Life, and Property Rock Christ and, the frightening Tadtad (Chop-Chop), which liked to pose its members for photographs with the severed heads of their victims. Vigilantes often carried magical amulets to ward off bullets, and their rituals were sometimes performed to loud rock music.

Domestic human rights groups, such as Task Force Detainees, and international monitors, such as Amnesty International, publicized incidents of torture. Amnesty International asserted that torture of communist rebels and sympathizers had become a common practice. One paramilitary group in 1988 responded to such criticism by shooting the Filipino regional chairman of Amnesty International. Six human rights lawyers were killed in the first three years of the Aquino government. More than 200 critics of the government were victims of extrajudicial executions. Many vigilantes carried pistols others were skilled with long, heavy knives called bolos.

Despite many documented abuses, United States and Philippine government officials have spoken in support of some vigilante groups. Aquino cited Alsa Masa's success in Davao as a legitimate exercise of People's Power. Her secretary of local government, Jaime Ferrer, ordered all local officials to set up civilian volunteer organizations or face dismissal. Ferrer was gunned down on August 2, 1987, for this and other anticommunist activities. The government made a distinction between ad hoc vigilante groups and the civilian volunteer organizations. The latter, which included Nation Watch (Bantay Bayan), were to conform to the following guidelines set forth on October 30, 1987, by the Department of National Defense: membership in the organizations was to be voluntary, members would be screened by the police, the organizations were to be defensive, and they were to eschew identification with individual landowners or politicians. Ramos fully supported the civilian volunteer organizations. He described their relationship to the uniformed military as "synergistic" and in 1989 grouped all 20,000 civilian volunteer organizations together under an umbrella organization called the National Alliance for Democracy. In reality, the lines between official and unofficial vigilante groups are often blurred. Large businesses have donated money to the National Alliance for Democracy and used its members as strikebreakers to counter leftist unions.

Data as of June 1991