Alleged coup organized by FSB

Starting from 1998, people from state security services came to power as Prime Ministers of Russia: a KGB veteran Yevgeny Primakov; former FSB Director Sergei Stepashin; and finally former FSB Director Vladimir Putin who was appointed in August 8, 1999.

In August 7, Shamil Basaev began incursion to Dagestan which was regarded by Anna Politkovskaya as a provocation intitiated from Moscow to start war in Chechnya, because Russian forces provided safe passage for Islamic fighters back to Chechnya. It was reported that Aleksander Voloshin from Yeltsin administration paid money to Shamil Basayev to stage this military operation (Basaev reportedly worked for Russian GRU at this time and earlier).

In September 4 a series of four Russian apartment bombings began. Three FSB agents were caught while planting a large bomb at the basement of an apartment complex in the town of Ryazan in September 22. That was last of the bombings. Russian Minister of Internal Affairs Rushailo congratulated police with preventing the terrorist act, but FSB Director Nikolai Patrushev had declared that the incident was a training exercise just an hour later, when he had learned that the FSB agents are caught.

The next day, Boris Yeltsin received a demand from 24 Russian governors to transfer all state powers to Prime Minister Vladimir Putin, according to Sergei Yushenkov Second Chechen War began on September 24. This war made Prime Minister Vladimir Putin very popular, although he was previously unknown to the public, and helped him to win a landslide victory in the presidential elections in March 26, 2000.

That was a successful coup d'état organized by the FSB to bring Vladimir Putin to power, according to former FSB officer Alexander Litvinenko, lawmaker Sergei Yushenkov, and journalist David Satter, a Johns Hopkins University and Hoover Institute scholar. All attempts to independently investigate the Russian apartment bombings were unsuccessful. Journalist Artyom Borovik died in a suspicious plane crash. Vice-chairman of Sergei Kovalev commission created to investigate the bombings Sergei Yushenkov was assassinated. Another member of this commission Yuri Shchekochikhin died presumably from poisoning by thallium. Investigator Mikhail Trepashkin hired by relatives of victims was arrested and convicted by Russian authorities for allegedly disclosing state secrets.

FSB as ruling political elite

According to former Russian Duma member Konstantin Borovoi, "Putin's appointment is the culmination of the KGB's crusade for power. This is its finale. Now the KGB runs the country." Olga Kryshtanovskaya, director of the Moscow-based Center for the Study of Elites, has found that up to 78% of 1,016 leading political figures in Russia have served previously in organizations affiliated with KGB or FSB. She said: "If in the Soviet period and the first post-Soviet period, the KGB and FSB people were mainly involved in security issues, now half are still involved in security but the other half are involved in business, political parties, NGOs, regional governments, even culture... They started to use all political institutions." "Like cockroaches spreading from a squalid apartment to the rest of the building, they have eventually gained a firm foothold everywhere," said Sergei Grigoryants, a Soviet dissident.

This situation is very similar to that of the former Soviet Union where all key positions in the government were occupied by members of the Communist Party. The KGB or FSB members usually remain in the "acting reserve" even if they formally leave the organization ("acting reserve" members receive second FSB salary, follow FSB instructions, and remain "above the law" being protected by the organization, according to Kryshtanovskaya). As Vladimir Putin said, "There is no such thing as a former KGB man". GRU defector and writer Victor Suvorov explained that members of Russian security services can leave such organizations only in a coffin, because they know too much. Soon after becoming prime minister of Russia, Putin also claimed that "A group of FSB colleagues dispatched to work undercover in the government has successfully completed its first mission.".

The idea about KGB as a leading political force rather than a security organization has been discussed by historian Abdurakhman Avtorkhanov, journalist John Barron, writer and former GRU officer Victor Suvorov, retired KGB Major General Oleg Kalugin, and Evgenia Albats. According to Avtorkhanov, "It is not true that the Political Bureau of the Central Committee of the Communist Party is a superpower... An absolute power thinks, acts and dictates for all of us. The name of the power — NKVD — MVD — MGB. ...Chekism in ideology, Chekism in practice. Chekism from top to bottom."

According to Albats, most KGB leaders, including Lavrenty Beria, Yuri Andropov, and Vladimir Kryuchkov, have always struggled for the power with the Communist Party and manipulated the communist leaders. Moreover, FSB has formal membership, military discipline, an extensive network of civilian informants, hardcore ideology, and support of population (60% of Russians trust FSB), which makes it a perfect totalitarian political party. However the FSB party does not advertise its leading role because the secrecy is an important advantage.

With regard to death of Aleksander Litvinenko, the highest-ranking Soviet Bloc intelligence defector, Lt. Gen. Ion Mihai Pacepa stated that there is "a band of over 6,000 former officers of the KGB — one of the most criminal organizations in history — who grabbed the most important positions in the federal and local governments, and who are perpetuating Stalin’s, Khrushchev’s, and Brezhnev’s practice of secretly assassinating people who stand in their way."

Suppression of internal dissent

Many Russian opposition lawmakers and investigative journalists have been assassinated while investigating corruption and alleged crimes conducted by FSB and state authorities: Sergei Yushenkov, ‎Yuri Shchekochikhin, Galina Starovoitova, Anna Politkovskaya, Alexander Litvinenko, Paul Klebnikov, Nadezhda Chaikova, Nina Yefimova, and many others. Former KGB officer Oleg Gordievsky believes that murders of writers Yuri Shchekochikhin (author of "Slaves of KGB"), Anna Politkovskaya, and Aleksander Litvinenko show that FSB has returned to the practice of political assassinations which were conducted in the past by Thirteenth KGB Department. Just before his death, Alexander Litvinenko accused Vladimir Putin of personally ordering the assassination of Anna Politkovskaya.

An increasing number of scientists have been accused of espionage and illegal technology exports by FSB during the last decade: researcher Igor Sutyagin, physicist Valentin Danilov, physical chemist Oleg Korobeinichev, academician Oskar Kaibyshev, and physicist Yury Ryzhov. Some other widely covered cases of political prosecution include investigator Mikhail Trepashkin and journalist Vladimir Rakhmankov. All these people are either under arrest or serve long jail sentences. Human rights groups also identified Mikhail Khodorkovsky as a political prisoner.

Ecologist and journalist Alexander Nikitin, who worked with Bellona Foundation, was accused of espionage. He published material exposing hazards posed by the Russian Navy's nuclear fleet. He was acquitted in 1999 after spending several years in prison (his case was sent for re-investigation 13 times while he remained in prison). Other cases of prosecution are the cases of investigative journalist and ecologist Grigory Pasko, Vladimir Petrenko who described danger posed by military chemical warfare stockpiles, and Nikolay Shchur, chairman of the Snezhinskiy Ecological Fund.

Other arrested people include Viktor Orekhov, a former KGB officer who assisted Soviet dissidents, Vladimir Kazantsev who disclosed illegal purchases of eavesdropping devices from foreign firms, and Vil Mirzayanov who had written that Russia was working on a nerve gas weapon.

Political dissidents from the former Soviet republics, such as Tajikistan and Uzbekistan, are often arrested by FSB and extradited to these countries for prosecution, despite to protests from international human rights organizations. Special services of Tajikistan, Uzbekistan, Turkmenistan and Azerbaidjan also kidnap people at the Russian territory, with the implicit approval of FSB.

There are credible reports that FSB use drugs to erase memory of people who had access to secret information.

Criticism of anti-terrorist operations

Use of excessive force by FSB spetsnaz was criticized with regard to resolving Moscow theater hostage crisis and Beslan hostage crisis. According to Sergey Kovalev, Russian government kills its citizens without any hesitation. He provided the following examples: murdering of hostages by the poison gas during Moscow theater hostage crisis; burning school children alive by spetsnaz soldiers who used RPO flamethrowers during Beslan school hostage crisis; crimes committed by death squads in Chechnya; and assassination of Zelimkhan Yandarbiyev. Anna Politkovskaya and Irina Hakamada, who conducted unofficial negotiations with terrorists, stated that the hostage takers were not going to use their bombs to kill the people and destroy the building during Moscow theater hostage crisis.

It is also possible that FSB has returned to the old NKVD practice of creating puppet rebel forces, as during the Trust Operation, Basmachi Revolt, or operations against the Ukrainian Insurgent Army Former FSB officer Aleksander Litvinenko stated in a June 2003 interview, with the Australian SBS television programme Dateline, that two of the Chechen terrorists involved in the 2002 Moscow theatre hostage crisis — whom he named as "Abdul the Bloody" and "Abu Bakar" — were working for the FSB, and that the agency manipulated the rebels into staging the attack. Litvinenko said: "[w]hen they tried to find [Abdul the Bloody and Abu Bakar] among the dead terrorists, they weren't there. The FSB got its agents out. So the FSB agents among Chechens organised the whole thing on FSB orders, and those agents were released." The story about FSB connections with the hostage takers was confirmed by Mikhail Trepashkin. Yulia Latynina and other journalists also accused FSB of staging many smaller terrorism acts, such as market place bombing in the city of Astrakhan, bus stops bombings in the city of Voronezh, and the blowing up the Moscow-Grozny train, whereas innocent people were convicted or killed. Journalist Boris Stomakhin claimed that bombing in Moscow metro in 2004 was probably organized by FSB agents rather than by the unknown man who called to Kavkaz Center and claimed his responsibility. Stomakin was arrested and imprisoned for writing this and other articles.

Many journalists and workers of international NGOs are reported to be kidnapped by FSB-affiliated forces in Chechnya who pretended to be Chechen terrorists: Andrei Babitsky from Radio Free Europe, Arjan Erkel and Kenneth Glack from Doctors Without Borders, and others.

According to Anna Politkovskaya, most of the "Islamic terrorism cases" were fabricated by the government, and the confessions have been obtained through the torture of innocent suspects. "The plight of those sentenced for Islamic terrorism today is the same as that of the political prisoners of the Gulag Archipelago... Russia continues to be infected by Stalinism", she said.

Alleged involvement in organized crime

Former FSB officer Aleksander Litvinenko accused FSB personnel of involvement in organized crime, such as drug trafficking and contract killings. It was noted that FSB, far from being a reliable instrument in the fight against organized crime, is institutionally a part of the problem, due not only to its co-optation and penetration by criminal elements, but to its own absence of a legal bureaucratic culture and use of crime as an instrument of state policy.

International affairs

FSB collaborates very closely with secret police services from some former Soviet Republics, especially Turkmenistan, Tajikistan, and Uzbekistan The FSB is accused of working to undermine governments of Baltic states and Georgia. During 2006 Georgian-Russian espionage controversy several Russian GRU officers were accused by Georgian authorities of preparations to commit sabotage and terrorist acts. Historian J. R. Nyquist believes that "The KGB president of Russia wants to reestablish the USSR. Whether America likes it or not, this very fact leads us to a new Cold War."

Chairman of the United Nations Special Commission Richard Butler found than many Russian state-controlled companies are involved in the Oil-for-Food Programme-related fraud. As a part of this affair, former FSB Director Yevgeny Primakov had received large kickbacks from Saddam Hussein according to Butler. KGB, FSB and Russian government had very close relationships with Saddam Hussein and Iraqi Intelligence Service Mukhabarat according to Yossef Bodansky, the Director of Research of the International Strategic Studies Association.