[14] A number of historians and investigative journalists have instead called the bombings a false flag attack perpetrated by Russian state security services to win public support for a new war in Chechnya and to boost the popularity of Vladimir Putin prior to the upcoming presidential elections.

[6][24] According to Amy Knight, "even more significant is the fact that a respected and influential Duma deputy, Konstantin Borovoi, was told on September 9, the day of the first Moscow apartment bombing, that there was to be a terrorist attack in the city.

Prior to his flight, Putin telephoned Clinton and claimed he had "every reason to believe" that Chechen extremists were not only behind the attacks but had links to the Al-Qaeda group which had perpetrated the bombings of the U.S. embassies in Nairobi and Dar es Salaam the previous year.

[70] Prime Minister Vladimir Putin signed a decree calling on law enforcement and other agencies to develop plans within three days to protect industry, transportation, communications, food processing centres and nuclear complexes.

[28] He said:[85] If the sacks which proved to contain explosive were noticed, that means there is a positive side to it, if only the fact that the public is reacting correctly to the events taking place in our country today.

... No panic, no sympathy for the bandits.On 23 September Natalia Yukhnova, a telephone service employee in Ryazan, tapped into a suspicious phone call to Moscow and overheard the following instruction: "Leave one at a time, there are patrols everywhere".

The gas analyser was of world-class quality, cost $20,000, and was maintained by a specialist who worked according to a strict schedule, making frequent prophylactic checks, because the device contained a radioactive source.

[100] After the newspaper report, FSB officers descended on Pinyayev's unit, accused them of divulging a state secret and told them, "You guys can't even imagine what serious business you’ve got yourselves tangled up in."

[46][104][105] However, FSB has declared later that the explosives used in the bombings were a mixture of aluminium powder, ammonium nitrate, TNT and sugar prepared by the perpetrators in a concrete mixer at a fertiliser factory in Urus-Martan, Chechnya.

[108] According to David Satter, the FSB changed the story about the type of explosive, since it was difficult to explain how huge amounts of RDX disappeared from the closely guarded Perm facility.

[109] On 9 September, an anonymous person, speaking with a Caucasian accent, phoned the Interfax news agency, saying that the blasts in Moscow and Buynaksk were "our response to the bombings of civilians in the villages in Chechnya and Dagestan.

According to the Russian State Prosecutor office,[107][125] all apartment bombings were executed under command of ethnic Karachay Achemez Gochiyayev and planned by Ibn al-Khattab and Abu Omar al-Saif, Arab militants fighting in Chechnya on the side of Chechen insurgents.

According to investigators, the explosives were prepared at a fertiliser factory in Urus-Martan Chechnya, by "mixing aluminium powder, nitre and sugar in a concrete mixer",[128] or by also putting there RDX and TNT.

[177] Trepashkin was unable to bring the alleged evidence to the court because he was arrested in October 2003 (on charges of illegal arms possession) and imprisoned in Nizhny Tagil, just a few days before he was to make his findings public.

[179] Amnesty International issued a statement that "there are serious grounds to believe that Mikhail Trepashkin was arrested and convicted under falsified criminal charges which may be politically motivated, in order to prevent him continuing his investigative and legal work related to the 1999 apartment bombings in Moscow and other cities".

[180] In a letter to Olga Konskaya, Trepashkin wrote that some time before the bombings, Moscow's Regional Directorate against Organized Crimes (RUOP GUVD) arrested several people for selling the explosive RDX.

[185] According to Alexander Goldfarb, Mr. Malashenko told him that Valentin Yumashev brought a warning from the Kremlin, one day before airing the show, promising in no uncertain terms that the NTV managers "should consider themselves finished" if they went ahead with the broadcast.

According to David Satter, Yuri Felshtinsky, Alexander Litvinenko, Vladimir Pribylovsky and Boris Kagarlitsky, the bombings were a successful false flag operation coordinated by the Russian state security services to win public support for a new full-scale war in Chechnya and to bring Putin to power.

(Felshtinsky & Litvinenko 2007) According to authors the bombings and other terrorist acts have been committed by Russian security services to justify the Second Chechen War and to bring Vladimir Putin to power.

According to the book, the murder of Litvinenko "gave credence to all his previous theories, delivering justice for the tenants of the bombed apartment blocks, the Moscow theater-goers, Sergei Yushenkov, Yuri Shchekochikhin, and Anna Politkovskaya, and the half-exterminated nation of Chechnya, exposing their killers for the whole world to see.

[209] The view about the bombings being organized and perpetrated by Russian state security services was originally put forward by journalist David Satter and historians Yuri Felshtinsky and Vladimir Pribylovsky, in co-authorship with Alexander Litvinenko.

[15][210] In her book Putin's Kleptocracy, historian Karen Dawisha summarized evidence related to the bombings and concluded that "to blow up your own innocent and sleeping people in your capital city is an action almost unthinkable.

"[85] In the September 2009 issue of GQ, veteran war correspondent Scott Anderson wrote about on Putin's role in the Russian apartment bombings, based in part on his interviews with Mikhail Trepashkin[214] The journal owner, Condé Nast, then took extreme measures[which?]

[216] Russian military analyst Pavel Felgenhauer noted that "The FSB accused Khattab and Gochiyaev, but oddly they did not point the finger at Chechen president Aslan Maskhadov's regime, which is what the war was launched against.

Mr. Putin ascended to the presidency in 2000 by pointing a finger at the Chechens for committing these crimes, launching a new military campaign in Chechnya, and riding a frenzy of public anger into office.

[222] In a speech to the Oxford Union on 12 March 2022, former MI6 officer Christopher Steele voiced support for the idea that the bombings were a false flag operation conducted by Russian security services in order to justify the war in Chechnya.

[225] Soldatov and Borogan noted that, according to Russian state security services, Achemez Gochiyaev was not an innocent businessman, but a leader of a local Islamist group since the mid-1990s, together with Dekkushev and Krymshamkhalov.

[222] Political scientist Ronald R. Pope in his review of David Satter's book Darkness at Dawn cited Kirill Pankratov's criticism, published as a contribution to Johnson's Russia List.

Regarding the apartment bombings, Pankratov argued that the Russian authorities did not need an additional justification to wage a war against Chechnya, in view of high-profile kidnappings and the invasion of Dagestan.

A draft Vaughn index, a document used by agencies to justify withholdings in FOIA cases, said that the release of that information had "the potential to inject friction into or cause serious damage" to relationships with the Russian government that were "vital to U.S. national security".