From its formation the agency has been headed by Colonel General Aleksandr Vladimirovich Starovoytov, formerly deputy chief of the USSR KGB's Government Communications Directorate.
Efforts to return FAPSI to the control of the Security Ministry, the Federal Counterintelligence Service, and the FSB continued for several years after the breakup of the KGB. In 1992 Barsukov and Korzhakov were able to mover from FAPSI to GUO the service that was subsequently named the Presidential Communications System. Posession of all these special communications automatic telephone exchangesgave GUO complete control over the presidential and government communications systems. Korzhakov also sought the de facto abolition (or subsumption) of the Agency.
Subsequently FAPSI transferred some operations communications systems to the Federal Counterintelligence Service, and Barsukov [the head of counterintelligence] further demanded that all operations and governmental intercity communications be transferred to his department. In the Summer of 1995 Barsukov prepared three draft edicts on the reassignment, the breakup, and the elimination of FAPSI.
When these formal efforts against FAPSI failed, the Presidential Security Service was said to have devised a plan to discredit "inconvenient" officials by collecting compromising materials on these leaders, including instituting criminal cases against them.
No less than half a dozen high- ranking functionaries have been forced to leave FAPSI due to financial scandals. FAPSI Financial and Economic Administration Director Vladimir Malinin resigned in the beginning of 1994 when an audit revealed a huge shortfall in the FAPSI. Two of his subordinates were caught during the commission of a crime. Chief of the armaments department Aleksey Domrayev and chief of the military-medical service Anatoliy Klyuyev have also resigned. And the agency's Deputy General Director Aleksandr Orlov went on leave and did not come back [he is rumored to have fled the country].
In March 1994 Valeriy Monastyretskiy, then head of the Roskomtekh firm which sold KGB property, was appointed Malinin's replacement as chief of the FAPSI Financial and Economic Administration. From 1980 he had worked in the KGB's - later FAPSI's Government Communications Directorate, and he left government service in 1992 to found several companies such as Roskomtekh with FAPSI financial assistance. On 12 April 1996 he was arrested on charges of misappropriating property and abuse of position. The FSB has alledged that Monastyretskiy began working for the German BND intelligence service not long before his arrest.
Monastyretskiy in turn charged that he was a victim of Korzhakov and Barsukov's criminal interests. He alleged that he had learned that Barsukov's Main Protection Administration [GUO] had purchased special eavesdropping equipment from companies connected with the CIA, to be installed in government offices. According to Monastyretskiy, when he attempted to prevent this pervasive surveillance of the Russian bureaucracy, he found himself targetted FSB military intelligence.
In the wake of the revelations about Monastyretskiy, compromising materials began appearing in the press challenging the rest of the Agency's leadership. A number of instances were documented in which senior FAPSI officials were living in extremely expensive apartments, or othewise engaged in financial irregularities. It was not by accident that the reporting focused on the extent to which FAPSI leaders obtained elite housing in the best areas of Moscow when regular FAPSI staff wait for years to obtain apartments. These scandals, or at least the publicity around it, seemed intended to discredit the FAPSI leadership in order to break up FAPSI and make it subordinate to the FSB on the eve of the presidential elections. Since FAPSI is intimately involved in surveillance and counter-surveillance activities, whoever controlled FAPSI possessed information, and thus could acquire power.
The 1996 reorganization of GUO apparently resulted in returning the facilities of the Government Communications Administration to FAPSI control. These initially supported just over 300 subscribers, compared with over 2,000 currently.