However, the program was soon enlarged to include disruption of the Socialist Workers Party (1961), the Ku Klux Klan (1964), African-American nationalist groups (including the Black Panther Party and the Nation of Islam (1967)), and the entire New Left socio-political movement, which included antiwar, community, and religious groups (1968).
A later investigation by the Senate's Church Committee (see below) stated that "COINTELPRO began in 1956, in part because of frustration with Supreme Court rulings limiting the Government's power to proceed overtly against dissident groups..." Congress and several court cases later concluded that the COINTELPRO operations against communist and socialist groups exceeded statutory limits on FBI activity and violated Constitutional guarantees of freedom of speech and association.
Supporters of the program argue that the project was rooted in the Bureau's knowledge that some domestic left-wing and radical organizations were manipulated by hostile foreign intelligence agencies. For example, the FBI had access to the Venona decrypts that showed the Soviet Union and its KGB manipulated and worked under the cover of the CPUSA for espionage purposes and to incite domestic unrest in the United States.
Some of the largest COINTELPRO campaigns targeted the Socialist Worker's Party, the Ku Klux Klan, the "New Left" (including several anti-war groups such as the Students for a Democratic Society and the Student Nonviolent Coordinating Committee), Black Liberation groups (such as the Black Panthers and the Republic of New Africa), Puerto Rican independence groups, the American Indian Movement and the Weather Underground.
The program was secret until 1971, when an FBI field office was burglarized by a group of left-wing radicals calling themselves the Citizens' Commission to Investigate the FBI. Several dossiers of files were taken and the information passed to news agencies. Within the year, Director Hoover declared that the centralized COINTELPRO was over, and that all future counterintelligence operations would be handled on a case-by-case basis.
Further documents were revealed in the course of separate lawsuits filed against the FBI by NBC correspondent Carl Stern, the SWP, and a number of other groups. A major investigation was launched in 1976 by the Select Committee to Study Governmental Operations with Respect to Intelligence Activities of the United States Senate, commonly referred to as the "Church Committee" for its chairman, Senator Frank Church of Idaho. However, millions of pages of documents remain unreleased, and many released documents are entirely censored.
In the Final Report of the Select Committee COINTELPRO was castigated in no uncertain terms:
"Many of the techniques used would be intolerable in a democratic society even if all of the targets had been involved in violent activity, but COINTELPRO went far beyond that...the Bureau conducted a sophisticated vigilante operation aimed squarely at preventing the exercise of First Amendment rights of speech and association, on the theory that preventing the growth of dangerous groups and the propagation of dangerous ideas would protect the national security and deter violence."
The Church Committee documented a history of the FBI being used for purposes of political repression as far back as World War I, through the 1920s, when they were charged with rounding up "anarchists and revolutionaries" for deportation, and then building from 1936 through 1976.
The FBI claims that it no longer undertakes COINTELPRO or COINTELPRO-like operations. However, critics claim that agency programs in the spirit of COINTELPRO target groups like the Committee in Solidarity with the People of El Salvador, Earth First! and the Anti-Globalization Movement.
1. "Infiltration: Agents and informers did not merely spy on political activists. Their main purpose was to discredit and disrupt. Their very presence served to undermine trust and scare off potential supporters. The FBI and police exploited this fear to smear genuine activists as agents." 
2. "Psychological Warfare From the Outside: The FBI and police used myriad other "dirty tricks" to undermine progressive movements. They planted false media stories and published bogus leaflets and other publications in the name of targeted groups. They forged correspondence, sent anonymous letters, and made anonymous telephone calls. They spread misinformation about meetings and events, set up pseudo movement groups run by government agents, and manipulated or strong-armed parents, employers, landlords, school officials and others to cause trouble for activists." 
3. "Harassment Through the Legal System: The FBI and police abused the legal system to harass dissidents and make them appear to be criminals. Officers of the law gave perjured testimony and presented fabricated evidence as a pretext for false arrests and wrongful imprisonment. They discriminatorily enforced tax laws and other government regulations and used conspicuous surveillance, 'investigative' interviews, and grand jury subpoenas in an effort to intimidate activists and silence their supporters."
4. "Extralegal Force and Violence: The FBI and police threatened, instigated, and themselves conducted break-ins, vandalism, assaults, and beatings. The object was to frighten dissidents and disrupt their movements. In the case of radical Black and Puerto Rican activists (and later Native Americans), these attacks—including political assassinations—were so extensive, vicious, and calculated that they can accurately be termed a form of official 'terrorism.'". 
The FBI also conducted "black bag jobs", warrantless surreptitious entries, against the targeted groups and their members.
Supporters of the FBI argue that the Bureau was convinced that there was such a threat of domestic subversion posed by radical groups that extraordinary efforts were required to forestall violence and revolutionary insurgency. Hoover was willing to use false claims to attack his political enemies. In one memo he wrote: "Purpose of counterintelligence action is to disrupt the Black Panther Party and it is immaterial whether facts exist to substantiate the charge."
In 1969 the FBI special agent in San Francisco wrote Hoover that his investigation of the Black Panther Party revealed that in his city, at least, the Black nationalists were primarily feeding breakfast to children. Hoover fired back a memo implying the career ambitions of the agent were directly related to his supplying evidence to support Hoover's view that the BPP was "a violence prone organization seeking to overthrow the Government by revolutionary means".
In one particularly controversial incident, civil rights worker Viola Liuzzo was killed in 1965 by a shot from a car in which four Ku Klux Klansmen were riding; one of the Klansmen was an undercover COINTELPRO operative. Afterward, COINTELPRO spread false rumors that she was a member of the Communist Party and had abandoned her children in order to have sexual relationships with African Americans involved in the civil rights movement. 
 Illegal surveillance
The Final report of the Church Committee concluded:
"Too many people have been spied upon by too many Government agencies and too much information has been collected. The Government has often undertaken the secret surveillance of citizens on the basis of their political beliefs, even when those beliefs posed no threat of violence or illegal acts on behalf of a hostile foreign power. The Government, operating primarily through secret informants, but also using other intrusive techniques such as wiretaps, microphone "bugs" surreptitious mail opening, and break-ins, has swept in vast amounts of information about the personal lives, views, and associations of American citizens. Investigations of groups deemed potentially dangerous -- and even of groups suspected of associating with potentially dangerous organizations -- have continued for decades, despite the fact that those groups did not engage in unlawful activity. Groups and individuals have been harassed and disrupted because of their political views and their lifestyles. Investigations have been based upon vague standards whose breadth made excessive collection inevitable. Unsavory and vicious tactics have been employed -- including anonymous attempts to break up marriages, disrupt meetings, ostracize persons from their professions, and provoke target groups into rivalries that might result in deaths. Intelligence agencies have served the political and personal objectives of presidents and other high officials. While the agencies often committed excesses in response to pressure from high officials in the Executive branch and Congress, they also occasionally initiated improper activities and then concealed them from officials whom they had a duty to inform.
Governmental officials -- including those whose principal duty is to enforce the law --have violated or ignored the law over long periods of time and have advocated and defended their right to break the law.
The Constitutional system of checks and balances has not adequately controlled intelligence activities. Until recently the Executive branch has neither delineated the scope of permissible activities nor established procedures for supervising intelligence agencies. Congress has failed to exercise sufficient oversight, seldom questioning the use to which its appropriations were being put. Most domestic intelligence issues have not reached the courts, and in those cases when they have reached the courts, the judiciary has been reluctant to grapple with them."