On 22 April 1999, several dozen Falun Gong practitioners were beaten and arrested in the city of Tianjin while staging a peaceful sit-in. The practitioners were told that the arrest order came from the Ministry of Public Security, and that those arrested could be released only with the approval of Beijing authorities.
At a meeting of the Politburo on 7 June 1999, Jiang described Falun Gong as a grave threat to Communist Party authority—"something unprecedented in the country since its founding 50 years ago"—and ordered the creation of a high-level committee to "get fully prepared for the work of disintegrating [Falun Gong]." Rumors of an impending crackdown began circulating throughout China, prompting demonstrations and petitions. The government publicly denied the reports, calling them "completely baseless" and offering assurances that it had never banned qigong activities.
Just after midnight on 20 July 1999, public security officers seized hundreds of Falun Gong practitioners from their homes in cities across China. Estimates on the number of arrests vary from several hundred to over 5,600. A Hong Kong newspaper reported that 50,000 individuals were detained in the first week of the crackdown. Four Falun Gong coordinators in Beijing were arrested and quickly tried on charges of "leaking state secrets". The Public Security Bureau ordered churches, temples, mosques, newspapers, media, courts and police to suppress Falun Gong. Three days of massive demonstrations by practitioners in some thirty cities followed. In Beijing and other cities, protesters were detained in sports stadiums. Editorials in state-run newspapers urged people to give up Falun Gong practice, and Communist Party members in particular were reminded that they were atheists and must not allow themselves to "become superstitious by continuing to practice Falun Gong."
Beginning in July 1999 Chinese authorities issued a number of notices and circulars prescribing measures to crack down on the Falun Gong and placing restrictions on the practice and expression of religious belief:
The Ministry of Justice required that lawyers seek permission before taking on Falun Gong cases, and called on them to "interpret the law in such a way as to conform to the spirit of the government's decrees." Additionally, on 5 November 1999 the Supreme People's Court issued a notice to all lower courts stating that it was their "political duty" to "resolutely impose severe punishment" against groups considered heretical, especially Falun Gong. It also required the courts at all levels to handle Falun Gong cases by following the direction of the Communist Party committees, thereby ensuring that Falun Gong cases would be judged based on political considerations, rather than evidence. Brian Edelman and James Richardson wrote that the SPC notice "does not comport well with a defendant's constitutional right to a defense, and it appears to assume guilt before a trial has taken place."
The Communist Party's campaign against Falun Gong was a turning point in the development of China's legal system, representing a "significant backward step" in the development of rule of law, according to Ian Dominson. In the 1990s the legal system was gradually becoming more professionalized, and a series of reforms in 1996–97 affirmed the principle that all punishments must be based on the rule of law. However, the campaign against Falun Gong would not have been possible if carried out within the narrow confines of China's existing criminal law. In order to persecute the group, in 1999 the judicial system reverted to being used as a political instrument, with laws being applied flexibly to advance the Communist Party's policy objectives. Edelman and Richardson write that "the Party and government's response to the Falun Gong movement violates citizens' right to a legal defense, freedom of religion, speech and assembly enshrined in the Constitution...the Party will do whatever is necessary to crush any perceived threat to its supreme control. This represents a move away from the rule of law and toward this historical Mao policy of 'rule by man.'"
State propaganda initially used the appeal of scientific rationalism to argue that Falun Gong's worldview was in "complete opposition to science" and communism. For example, the People's Daily newspaper asserted on 27 July 1999 that the fight against Falun Gong "was a struggle between theism and atheism, superstition and science, idealism and materialism." Other editorials declared that Falun Gong's "idealism and theism" are "absolutely contradictory to the fundamental theories and principles of Marxism," and that the "'truth, kindness and forbearance' principle preached by [Falun Gong] has nothing in common with the socialist ethical and cultural progress we are striving to achieve." Suppressing Falun Gong was presented as a necessary step to maintaining the "vanguard role" of the Communist Party in Chinese society.
Despite Party efforts, initial charges leveled against Falun Gong failed to elicit widespread popular support for the persecution of the group. In October 1999, three months after the persecution began, the Supreme People's Court issued a judicial interpretation classifying Falun Gong as a xiejiao. A broad translation of that term is "heretical teaching" or "heterodox teaching", but during the anti–Falun Gong propaganda campaign it was rendered as "cult" or "evil cult" in English. In the context of imperial China, the term "xiejiao" was used to refer to non-Confucian religions, though in the context of Communist China, it has been used to target religious organizations that do not submit to the authority of the Communist Party. Julia Ching writes that the "evil cult" label was defined by an atheist government "on political premises, not by any religious authority", and was used by the authorities to make previous arrests and imprisonments constitutional.
The Foreign Correspondents' Club of China has complained about their members being "followed, detained, interrogated and threatened" for reporting on the crackdown on Falun Gong. Foreign journalists covering a clandestine Falun Gong news conference in October 1999 were accused by the Chinese authorities of "illegal reporting". Journalists from Reuters, the New York Times, the Associated Press and a number of other organisations were interrogated by police, forced to sign confessions, and had their work and residence papers temporarily confiscated. Correspondents also complained that television satellite transmissions were interfered with while being routed through China Central Television. Amnesty International states that "a number of people have received prison sentences or long terms of administrative detention for speaking out about the repression or giving information over the Internet."
The Kilgour-Matas report called attention to the extremely short wait times for organs in China—one to two weeks for a liver compared with 32.5 months in Canada—indicating that organs were being procured on demand. A significant increase in the number of annual organ transplants in China beginning in 1999, corresponded with the onset of the persecution of Falun Gong. Despite very low levels of voluntary organ donation, China performs the second-highest number of transplants per year. Kilgour and Matas also presented incriminating material from Chinese transplant center web sites advertising the immediate availability of organs from living donors, as well as transcripts of telephone interviews in which hospitals told prospective transplant recipients that they could obtain Falun Gong organs. An updated version of their report was published as a book in 2009. Kilgour followed up on this investigation in a 680-page 2016 report.
From 1999 to 2013, the vast majority of detained Falun Gong practitioners were held in reeducation through labor (RTL) camps—a system of administrative detention where people can be imprisoned without trial for up to four years.
The government's use of "brainwashing sessions" began in 1999, but the network of transformation centers expanded nationwide in January 2001 when the central 610 Office mandated that all government bodies, work units, and corporations use them. The Washington Post reported "neighborhood officials have compelled even the elderly, people with disabilities and the ill to attend the classes. Universities have sent staff to find students who had dropped out or been expelled for practicing Falun Gong, and brought them back for the sessions. Other members have been forced to leave sick relatives" to attend the reeducation sessions. After the closure of the RTL system in 2013, authorities leaned more heavily on the transformation centers to detain Falun Gong practitioners. After the Nanchong RTL center in Sichuan province was closed, for example, at least a dozen of the Falun Gong practitioners detained there were sent directly to a local transformation center. Some former RTL camps have simply been renamed and converted into transformation centers.
Since 1999, several thousand Falun Gong practitioners have been sentenced to prisons through the criminal justice system. Most of the charges against Falun Gong practitioners are for political offenses such as "disturbing social order," "leaking state secrets," "subverting the socialist system," or "using a heretical organization to undermine the implementation of the law"—a vaguely worded provision used to prosecute, for instance, individuals who used the Internet to disseminate information about Falun Gong.
Since July 1999, civil servants and Communist Party members have been forbidden from practicing Falun Gong. Workplaces and schools were enjoined to participate in the struggle against Falun Gong by pressuring recalcitrant Falun Gong believers to renounce their beliefs, sometimes sending them to special reeducation classes to be "transformed". Failure to do so has results in lost wages, pensions, expulsion, or termination from jobs.
Falun Gong's response to the persecution in China began in July 1999 with appeals to local, provincial, and central petitioning offices in Beijing. It soon progressed to larger demonstrations, with hundreds of Falun Gong practitioners traveling daily to Tiananmen Square to perform Falun Gong exercises or raise banners in defense of the practice. These demonstrations were invariably broken up by security forces, and the practitioners involved were arrested—sometimes violently—and detained. By 25 April 2000, a total of more than 30,000 practitioners had been arrested on the square; seven hundred Falun Gong followers were arrested during a demonstration in the square on 1 January 2001. Public protests continued well into 2001. Writing for The Wall Street Journal, Ian Johnson wrote that "Falun Gong faithful have mustered what is arguably the most sustained challenge to authority in 50 years of Communist rule."